{ "_id": "6a13f099acfb0bcc41d30588", "Package": "wrMisc", "Version": "2.0.2", "Title": "Analyze Experimental High-Throughput (Omics) Data", "Authors@R": "person(\"Wolfgang\", \"Raffelsberger\", email = \"w.raffelsberger@gmail.com\", role = c(\"aut\", \"cre\"))", "Author": "Wolfgang Raffelsberger [aut, cre]", "Maintainer": "Wolfgang Raffelsberger ", "Description": "The efficient treatment and convenient analysis of\nexperimental high-throughput (omics) data gets facilitated\nthrough this collection of diverse functions. Several functions\naddress advanced object-conversions, like manipulating lists of\nlists or lists of arrays, reorganizing lists to arrays or into\nseparate vectors, merging of multiple entries, etc. Another set\nof functions provides speed-optimized calculation of standard\ndeviation (sd), coefficient of variance (CV) or standard error\nof the mean (SEM) for data in matrixes or means per line with\nrespect to additional grouping (eg n groups of replicates). A\ngroup of functions facilitate dealing with non-redundant\ninformation, by indexing unique, adding counters to redundant\nor eliminating lines with respect redundancy in a given\nreference-column, etc. Help is provided to identify very\nclosely matching numeric values to generate (partial) distance\nmatrixes for very big data in a memory efficient manner or to\nreduce the complexity of large data-sets by combining very\nclose values. Other functions help aligning a matrix or\ndata.frame to a reference using partial matching or to mine an\nexperimental setup to extract patterns of replicate samples.\nMany times large experimental datasets need some additional\nfiltering, adequate functions are provided. Convenient data\nnormalization is supported in various different modes,\nparameter estimation via permutations or boot-strap as well as\nflexible testing of multiple pair-wise combinations using the\nframework of 'limma' is provided, too. Batch reading (or\nwriting) of sets of files and combining data to arrays is\nsupported, too.", "VignetteBuilder": "knitr", "License": "GPL-3", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-25 06:44:03 UTC", "User": "root" }, "Repository": "https://wraff.r-universe.dev", "Date/Publication": "2026-04-29 11:56:52 UTC", "RemoteUrl": "https://github.com/cran/wrMisc", "RemoteRef": "HEAD", "RemoteSha": "eb2f7d0663afa382a21011f2bc6afc1367c3829e", "MD5sum": "7afe2b159f5be398ea87df3aa417e5f5", "_user": "wraff", "_type": "src", "_file": "wrMisc_2.0.2.tar.gz", "_fileid": "735e2787b6d07248fbe094c4c94dae305e2343112ae7d8ac6707440e94c62989", "_filesize": 2071686, "_sha256": "735e2787b6d07248fbe094c4c94dae305e2343112ae7d8ac6707440e94c62989", "_created": "2026-05-25T06:44:03.000Z", "_published": "2026-05-25T06:47:53.631Z", "_distro": "noble", "_jobs": [ { "job": 77668682356, "time": 173, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", 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arrays in list", "topics": [ ".arrLstSEM" ] }, { "page": "dot-asDF2", "title": "Convert anything to data.frame", "topics": [ ".asDF2" ] }, { "page": "dot-breakInSer", "title": "Get series of values after last discontinuity", "topics": [ ".breakInSer" ] }, { "page": "dot-bringToCtr", "title": "Bring most extreme to center", "topics": [ ".bringToCtr" ] }, { "page": "dot-checkArgNa", "title": "Check argument names", "topics": [ ".checkArgNa" ] }, { "page": "dot-checkConsistentArrList", "title": "Check list of arrays for consistent dimensions of all arrays", "topics": [ ".checkConsistentArrList" ] }, { "page": "dot-checkConvt2Vect", "title": "Convert To Simple Vector (similar to unlist)", "topics": [ ".checkConvt2Vect" ] }, { "page": "dot-checkFactor", "title": "Check Factor", "topics": [ ".checkFactor" ] }, { "page": "dot-checkFileNameExtensions", "title": "Check File Name Extensions Function for checking file-names.", "topics": [ ".checkFileNameExtensions" ] }, { "page": "dot-checkLegendLoc", "title": "Check argument for Location of legend", "topics": [ ".checkLegendLoc" ] }, { "page": "dot-checkLmConfInt", "title": "Compare 'dat' to confindence interval of linare model 'lMod' (eg from lm())", "topics": [ ".checkLmConfInt" ] }, { "page": "dot-checkRegrArguments", "title": "Check regression arguments", "topics": [ ".checkRegrArguments" ] }, { "page": "dot-chooseGrpCol", "title": "Automatic choice of colors", "topics": [ ".chooseGrpCol" ] }, { "page": "dot-combineListAnnot", "title": "Combine annotation information from list of matrixes", "topics": [ ".combineListAnnot" ] }, { "page": "dot-compareByDiff", "title": "Compare by distance/difference", "topics": [ ".compareByDiff" ] }, { "page": "dot-compareByLogRatio", "title": "Compare by log-ratio", "topics": [ ".compareByLogRatio" ] }, { "page": "dot-compareByPPM", "title": "Compare by PPM", "topics": [ ".compareByPPM" ] }, { "page": "dot-complCols", "title": "Search (complementing) Columns For Best 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"dot-growTree", "title": "Grow Tree", "topics": [ ".growTree" ] }, { "page": "dot-insp1dimByClustering", "title": "Segment (1-dim vector) 'dat' into clusters", "topics": [ ".insp1dimByClustering" ] }, { "page": "dot-inspectHeader", "title": "Inspect 'matr' and check if 1st line can be used/converted as header", "topics": [ ".inspectHeader" ] }, { "page": "dot-keepCenter1d", "title": "Refine/filter 'dat1' (1dim dataset, eg cluster) with aim of keeping center of data", "topics": [ ".keepCenter1d" ] }, { "page": "dot-keepFiniteCol", "title": "Remove all columns where all data are not finite", "topics": [ ".keepFiniteCol" ] }, { "page": "dot-mayBeNum", "title": "Check if vector may be numeric content", "topics": [ ".mayBeNum" ] }, { "page": "dot-medianSpecGrp", "title": "Rescale respective to specific group", "topics": [ ".medianSpecGrp" ] }, { "page": "dot-mergeMatrices", "title": "Merge Multiple Matrices (main)", "topics": [ ".mergeMatrices" ] }, { "page": "dot-minDif", "title": "find closest neighbour to numeric vector", "topics": [ ".minDif" ] }, { "page": "dot-neigbDis", "title": "Distances beteenw sorted points of 2-columns", "topics": [ ".neigbDis" ] }, { "page": "dot-normalize", "title": "Main Normalization function", "topics": [ ".normalize" ] }, { "page": "dot-normConstSlope", "title": "Normalize Columns Of 2-dim Matrix To Common Linear Regression Fit", "topics": [ ".normConstSlope" ] }, { "page": "dot-pasteCols", "title": "Paste-concatenate all columns of matrix", "topics": [ ".pasteCols" ] }, { "page": "dot-plotCountPie", "title": "Pie plot for counting results", "topics": [ ".plotCountPie" ] }, { "page": "dot-plusLowerCaps", "title": "Add lower caps to character vector", "topics": [ ".plusLowerCaps" ] }, { "page": "dot-predRes", "title": "Calculate residues of (2-dim) linear model 'lMod'-prediction of/for 'dat'", "topics": [ ".predRes" ] }, { "page": "dot-raiseColLowest", "title": "Raise all values close to lowest value", "topics": [ ".raiseColLowest" ] }, { "page": "dot-removeCol", "title": "Remove columns indicated by col-number", "topics": [ ".removeCol" ] }, { "page": "dot-removeEmptyCol", "title": "Search for (empty) columns conaining only entries defined in 'searchFields' and remove such columns", "topics": [ ".removeEmptyCol" ] }, { "page": "dot-replSpecChar", "title": "Replace Special Characters", "topics": [ ".replSpecChar" ] }, { "page": "dot-retain1stPart", "title": "Trim character string: keep only text before 'sep'", "topics": [ ".retain1stPart" ] }, { "page": "dot-rowGrpCV", "title": "row group CV (main)", "topics": [ ".rowGrpCV" ] }, { "page": "dot-rowGrpMeans", "title": "row group mean (main)", "topics": [ ".rowGrpMeans" ] }, { "page": "dot-rowGrpSds", "title": "row group sd (main)", "topics": [ ".rowGrpSds" ] }, { "page": "dot-rowGrpSums", "title": "row group rowSums per group (main)", "topics": [ ".rowGrpSums" ] }, { "page": "dot-rowNorm", "title": "Row-normalization Procedure On Matrix Or Data.frame (main)", "topics": [ ".rowNorm" ] }, { "page": "dot-rowNormFact", "title": "Obtain Normalization Factor (main)", "topics": [ ".rowNormFact" ] }, { "page": "dot-scale01", "title": "Scale between 0 and 1 (main)", "topics": [ ".scale01" ] }, { "page": "dot-scaleSpecGrp", "title": "Rescale respective to specific group", "topics": [ ".scaleSpecGrp" ] }, { "page": "dot-scaleXY", "title": "Scale between min and max value (main)", "topics": [ ".scaleXY" ] }, { "page": "dot-seqCutStr", "title": "Cut string to get all variants from given start with min length, depreciated", "topics": [ ".seqCutStr" ] }, { "page": "dot-setLowestTo", "title": "Set lowest value to given value", "topics": [ ".setLowestTo" ] }, { "page": "dot-sortMid", "title": "Choose most frequent or middle of sorted vector", "topics": [ ".sortMid" ] }, { "page": "dot-stackArray", "title": "Reorganize array by reducing dimension 'byDim' (similar to stack() for data-frames)", "topics": [ ".stackArray" ] }, { "page": "dot-summarizeCols", "title": "Summarize columns of matrix (or data.frame) 'x' using apply (main)", "topics": [ ".summarizeCols" ] }, { "page": "dot-trimFromEnd", "title": "Trim from end (Deprecated)", "topics": [ ".trimFromEnd" ] }, { "page": "dot-trimFromStart", "title": "Trim from start (Deprecated)", "topics": [ ".trimFromStart" ] }, { "page": "dot-trimLeft", "title": "Trim From Left Side", "topics": [ ".trimLeft" ] }, { "page": "dot-trimRight", "title": "Trim From Right Side", "topics": [ ".trimRight" ] }, { "page": "dot-uniqueWName", "title": "Check regression arguments", "topics": [ ".uniqueWName" ] }, { "page": "dot-vector2Matr", "title": "Convert numeric vector to matrix", "topics": [ ".vector2Matr" ] }, { "page": "addBeforFileExtension", "title": "Add text before file-extension", "topics": [ "addBeforFileExtension" ] }, { "page": "adjBy2ptReg", "title": "Linear rescaling of numeric vertor or matrix", "topics": [ "adjBy2ptReg" ] }, { "page": "adjustUnitPrefix", "title": "Adjust Value With Different Decimal Prefixes To Single Prefix Plus Unit", "topics": [ "adjustUnitPrefix" ] }, { "page": "appendNR", "title": "Append vectors or lists, without duplcating common elements", "topics": [ "appendNR" ] }, { "page": "arrayCV", "title": "CV of array", "topics": [ "arrayCV" ] }, { "page": "asSepList", "title": "Organize Data as Separate List-Entries", "topics": [ "asSepList" ] }, { "page": "buildTree", "title": "Connect edges to from tree and extract all possible branches", "topics": [ "buildTree" ] }, { "page": "cbindNR", "title": "cbind to non-redundant", "topics": [ "cbindNR" ] }, { "page": "checkAvSd", "title": "Check how multiple groups of data separate or overlap based on mean +/- sd", "topics": [ "checkAvSd" ] }, { "page": "checkFilePath", "title": "Verify File-name If Existing (in specified path), If Has Proper Extension Or Select Files With Proper Extension From Given Path", "topics": [ "checkFilePath" ] }, { "page": "checkGrpOrder", "title": "checkGrpOrder", "topics": [ "checkGrpOrder" ] }, { "page": "checkGrpOrderSEM", "title": "Check order of multiple groups including non-overlapping SEM-margins", "topics": [ "checkGrpOrderSEM" ] }, { "page": "checkSimValueInSer", "title": "Check for similar values in series", "topics": [ "checkSimValueInSer" ] }, { "page": "checkStrictOrder", "title": "Check for strict (ascencing or descending) order", "topics": [ "checkStrictOrder" ] }, { "page": "checkUnitPrefix", "title": "Check For Common Unit-Name in Text", "topics": [ "checkUnitPrefix" ] }, { "page": "checkVectLength", "title": "Check length of vector", "topics": [ "checkVectLength" ] }, { "page": "chooseGroupNames", "title": "Choose Column Most Likely For Sample-Names", "topics": [ "chooseGroupNames" ] }, { "page": "cleanReplicates", "title": "Replace Most Distant Values by NA", "topics": [ "cleanReplicates" ] }, { "page": "closeMatchMatrix", "title": "Reorganize results of search for close (similar) values in matrix-view", "topics": [ "closeMatchMatrix" ] }, { "page": "coinPermTest", "title": "Compare Means Of Two Vectors By Permutation Test", "topics": [ "coinPermTest" ] }, { "page": "colCVs", "title": "rowCVs", "topics": [ "colCVs" ] }, { "page": "colMedSds", "title": "Standard Error Of Median For Each Column By Bootstrap", "topics": [ "colMedSds" ] }, { "page": "colorAccording2", "title": "Transform Numeric Values To Color-Gradient", "topics": [ "colorAccording2" ] }, { "page": "colSds", "title": "sd for each column", "topics": [ "colSds" ] }, { "page": "combinatIntTable", "title": "Planing for making all multiplicative combinations", "topics": [ "combinatIntTable" ] }, { "page": "combineAsN", "title": "Combine Vectors From List And Return Basic Count Statistics", "topics": [ "combineAsN" ] }, { "page": "combineByEitherFactor", "title": "Create factor-like column regrouping data regrouping simultaneaously by two factors", "topics": [ "combineByEitherFactor" ] }, { "page": "combineOverlapInfo", "title": "Find And Combine Points Located Very Close In x/y Space", "topics": [ "combineOverlapInfo" ] }, { "page": "combineRedBasedOnCol", "title": "Combine/reduce redundant lines based on specified column", "topics": [ "combineRedBasedOnCol" ] }, { "page": "combineRedundLinesInList", "title": "Combine Redundant Lines In List", "topics": [ "combineRedundLinesInList" ] }, { "page": "combineRedundLinesInListAcRef", "title": "Combine Redundant Lines In List, Deprecated", "topics": [ "combineRedundLinesInListAcRef" ] }, { "page": "combineReplFromListToMatr", "title": "Combine replicates from list to matrix", "topics": [ "combineReplFromListToMatr" ] }, { "page": "combineSingleT", "title": "Get All Combinations With TRUE From Each Column", "topics": [ "combineSingleT" ] }, { "page": "completeArrLst", "title": "Complete list of arrays for same dimensions", "topics": [ "completeArrLst" ] }, { "page": "concatMatch", "title": "Value Matching With Option For Concatenated Terms", "topics": [ "concatMatch" ] }, { "page": "confInt", "title": "Confidence Interval To Given Alpha", "topics": [ "confInt" ] }, { "page": "contribToContigPerFrag", "title": "Characterize individual contribution of single edges in tree-structures", "topics": [ "contribToContigPerFrag" ] }, { "page": "conv01toColNa", "title": "Convert matrix of integer to matrix of x-times repeated column-names", "topics": [ "conv01toColNa" ] }, { "page": "convColorToTransp", "title": "Assign new transparency to given colors", "topics": [ "convColorToTransp" ] }, { "page": "convMatr2df", "title": "Convert matrix (eg with redundant) row-names to data.frame", "topics": [ "convMatr2df" ] }, { "page": "convPairwiseSetup", "title": "Check Comparison-Choice", "topics": [ "convPairwiseSetup" ] }, { "page": "convToNum", "title": "Convert Vector To Numeric", "topics": [ "convToNum" ] }, { "page": "coordOfFilt", "title": "get coordinates of values/points in matrix according to filtering condition", "topics": [ "coordOfFilt" ] }, { "page": "correctToUnique", "title": "Correct vector to unique", "topics": [ "correctToUnique" ] }, { "page": "correctWinPath", "title": "Correct Mixed Slash And Backslash In File-Path", "topics": [ "correctWinPath" ] }, { "page": "countCloseToLimits", "title": "Count From Two Vectors Number Of Values Close Within Given Limits", "topics": [ "countCloseToLimits" ] }, { "page": "countSameStartEnd", "title": "Count Same Start- And End- Sites Of Edges (Or Fragments)", "topics": [ "countSameStartEnd" ] }, { "page": "cutArrayInCluLike", "title": "Cut 3-dim array in list of matrixes (or arrays) similar to organizing into clusters", "topics": [ "cutArrayInCluLike" ] }, { "page": "cutAtMultSites", "title": "Cut character-vector at multiple sites", "topics": [ "cutAtMultSites" ] }, { "page": "cutToNgrp", "title": "Cut numeric vector to n groups (ie convert to factor)", "topics": [ "cutToNgrp" ] }, { "page": "diffCombin", "title": "Compute Matrix Of Differences For All Pairwise Combinations Of Numeric Vector", "topics": [ "diffCombin" ] }, { "page": "diffPPM", "title": "Difference in ppm between numeric values", "topics": [ "diffPPM" ] }, { "page": "elimCloseCoord", "title": "Eliminate close (overlapping) points (in x & y space)", "topics": [ "elimCloseCoord" ] }, { "page": "equLenNumber", "title": "Equal character-length number", "topics": [ "equLenNumber" ] }, { "page": "exclExtrValues", "title": "Exclude extreme values (based on distance to mean)", "topics": [ "exclExtrValues" ] }, { "page": "exponNormalize", "title": "Normalize By Adjusting Exponent", "topics": [ "exponNormalize" ] }, { "page": "extr1chan", "title": "Extract Just One Series, ie One Channel, Of List Of Arrays", "topics": [ "extr1chan" ] }, { "page": "extractLast2numericParts", "title": "Extract Last Two Numeric Parts From Character Vector", "topics": [ "extractLast2numericParts" ] }, { "page": "extrColsDeX", "title": "Flexible extraction of columns", "topics": [ "extrColsDeX" ] }, { "page": "extrNumericFromMatr", "title": "Extract numeric part of matrix or data.frame", "topics": [ "extrNumericFromMatr" ] }, { "page": "extrSpcText", "title": "Extract specific text", "topics": [ "extrSpcText" ] }, { "page": "filt3dimArr", "title": "Filter three-dimensional array of numeric data", "topics": [ "filt3dimArr" ] }, { "page": "filterLiColDeList", "title": "Filter lines(rows) and/or columns from all suitable elements of list", "topics": [ "filterLiColDeList" ] }, { "page": "filterList", "title": "Filter for unique elements", "topics": [ "filterList" ] }, { "page": "filterNetw", "title": "Filter nodes & edges for extracting networks This function allows extracting and filtering network-data based on fixed threshold ('limInt') and add sandwich-nodes (nodes inter-connecting initial nodes) out of node-based queries.", "topics": [ "filterNetw" ] }, { "page": "filtSizeUniq", "title": "Filter For UniqueElements", "topics": [ "filtSizeUniq" ] }, { "page": "findCloseMatch", "title": "Find Close Numeric Values Between Two Vectors", "topics": [ "findCloseMatch" ] }, { "page": "findHeadAndTail", "title": "Find Group-Names In Pairwise Combined And Isolate Separator", "topics": [ "findHeadAndTail" ] }, { "page": "findRepeated", "title": "Find repeated elements", "topics": [ "findRepeated" ] }, { "page": "findSimilFrom2sets", "title": "Find similar numeric values from two vectors/matrixes", "topics": [ "findSimilFrom2sets" ] }, { "page": "findUsableGroupRange", "title": "Select groups within given range", "topics": [ "findUsableGroupRange" ] }, { "page": "firstLineOfDat", "title": "Filter matrix to keep only first of repeated lines", "topics": [ "firstLineOfDat" ] }, { "page": "firstOfRepeated", "title": "Find first of repeated elements", "topics": [ "firstOfRepeated" ] }, { "page": "firstOfRepLines", "title": "Reduce To First Occurance Of Repeated Lines", "topics": [ "firstOfRepLines" ] }, { "page": "fuseAnnotMatr", "title": "Fuse annotation matrix to initial matrix", "topics": [ "fuseAnnotMatr" ] }, { "page": "fuseCommonListElem", "title": "Fuse content of list-elements with redundant (duplicated) names", "topics": [ "fuseCommonListElem" ] }, { "page": "fusePairs", "title": "Fuse pairs to generate cluster-names", "topics": [ "fusePairs" ] }, { "page": "get1stOfRepeatedByCol", "title": "Get First Of Repeated By Column", "topics": [ "get1stOfRepeatedByCol" ] }, { "page": "getPairwiseSetup", "title": "Extract Pairwise Testing Setup", "topics": [ "getPairwiseSetup" ] }, { "page": "getPWseparator", "title": "Identify Separator In Pairwise Group-Names Or Find Separator For Use With Pairwise Group-Names This function allows identifing separator used when pairwise groups are presented.", "topics": [ "getPWseparator" ] }, { "page": "getValuesByUnique", "title": "Print matrix-content as plot", "topics": [ "getValuesByUnique" ] }, { "page": "gitDataUrl", "title": "Convert GitHub Url-Name For Reading In Raw-Mode", "topics": [ "gitDataUrl" ] }, { "page": "htmlSpecCharConv", "title": "Html Special Character Conversion", "topics": [ "htmlSpecCharConv" ] }, { "page": "indexGroupsFromPW", "title": "Index Names Of Groups From Vector Of Concatenated Pairwise Group-Names", "topics": [ "indexGroupsFromPW" ] }, { "page": "keepCommonText", "title": "Extract Longest Common Text Out Of Character Vector", "topics": [ "keepCommonText" ] }, { "page": "levIndex", "title": "Transform (factor) levels into index", "topics": [ "levIndex" ] }, { "page": "linModelSelect", "title": "Test Multiple Starting Levels For Linear Regression Model, Select Best And Plot", "topics": [ "linModelSelect" ] }, { "page": "linRegrParamAndPVal", "title": "Fit linear regression, return parameters and p-values", "topics": [ "linRegrParamAndPVal" ] }, { "page": "listBatchReplace", "title": "Replacements in list", "topics": [ "listBatchReplace" ] }, { "page": "listGroupsByNames", "title": "Organize Values Into List And Sort By Names", "topics": [ "listGroupsByNames" ] }, { "page": "lmSelClu", "title": "Run lm on segmented data (from clustering)", "topics": [ "lmSelClu" ] }, { "page": "lrbind", "title": "rbind on lists", "topics": [ "lrbind" ] }, { "page": "makeMAList", "title": "Make MA-List Object", "topics": [ "makeMAList" ] }, { "page": "makeNRedMatr", "title": "Make non-redundant matrix", "topics": [ "makeNRedMatr" ] }, { "page": "matchMatrixLinesToRef", "title": "Match All Lines of Matrix To Reference Note", "topics": [ "matchMatrixLinesToRef" ] }, { "page": "matchNamesWithReverseParts", "title": "Value Matching with optional reversing of sub-parts of non-matching elements", "topics": [ "matchNamesWithReverseParts" ] }, { "page": "matchSampToPairw", "title": "Match Names To Concatenated Pairs Of Names", "topics": [ "matchSampToPairw" ] }, { "page": "matr2list", "title": "Transform columns of matrix to list of vectors", "topics": [ "matr2list" ] }, { "page": "mergeMatrices", "title": "Merge Multiple Matrices", "topics": [ "mergeMatrices" ] }, { "page": "mergeMatrixList", "title": "Merge Multiple Matrices from List", "topics": [ "mergeMatrixList" ] }, { "page": "mergeSelCol", "title": "Merge selected columns out of 2 matrix or data.frames", "topics": [ "mergeSelCol" ] }, { "page": "mergeSelCol3", "title": "mergeSelCol3", "topics": [ "mergeSelCol3" ] }, { "page": "mergeVectors", "title": "Merge Named Vectors", "topics": [ "mergeVectors" ] }, { "page": "mergeW2", "title": "Extended version of merge for multiple objects (even without rownames)", "topics": [ "mergeW2" ] }, { "page": "minDiff", "title": "Minimum distance/difference between values", "topics": [ "minDiff" ] }, { "page": "moderTest2grp", "title": "Moderated Pairwise t-test From Limma", "topics": [ "moderTest2grp" ] }, { "page": "moderTestXgrp", "title": "Multiple Moderated Pairwise t-tests From limma", "topics": [ "moderTestXgrp" ] }, { "page": "multiCharReplace", "title": "Multiple replacement of entire character elements in simple vector, matrix or data.frame", "topics": [ "multiCharReplace" ] }, { "page": "multiMatch", "title": "Simple Multi-to-Multi Matching of (Concatenated) Terms", "topics": [ "multiMatch" ] }, { "page": "naOmit", "title": "Fast na.omit", "topics": [ "naOmit" ] }, { "page": "nFragments", "title": "Number Of Fragments After Cut At Specific Character(s) Within Size-range", "topics": [ "nFragments" ] }, { "page": "nFragments0", "title": "Number Of Fragments After Cut At Specific Character(s)", "topics": [ "nFragments0" ] }, { "page": "nNonNumChar", "title": "Count number of non-numeric characters", "topics": [ "nNonNumChar" ] }, { "page": "nonAmbiguousMat", "title": "Transform matrix to non-ambiguous matrix (in respect to given column)", "topics": [ "nonAmbiguousMat" ] }, { "page": "nonAmbiguousNum", "title": "Make numeric vector non-ambiguous (ie unique)", "topics": [ "nonAmbiguousNum" ] }, { "page": "nonredDataFrame", "title": "Filter for unique elements", "topics": [ "nonredDataFrame" ] }, { "page": "nonRedundLines", "title": "Non-Redundant Lines Of Matrix", "topics": [ "nonRedundLines" ] }, { "page": "normalizeThis", "title": "Normalize Data In Various Modes", "topics": [ "normalizeThis" ] }, { "page": "numPairDeColNames", "title": "Extract pair of numeric values from vector or column-names", "topics": [ "numPairDeColNames" ] }, { "page": "orderMatrToRef", "title": "Order Lines of Matrix According to Reference (Character) Vector", "topics": [ "orderMatrToRef" ] }, { "page": "organizeAsListOfRepl", "title": "(re)organize data of (3-dim) array as list of replicates", "topics": [ "organizeAsListOfRepl" ] }, { "page": "packageDownloadStat", "title": "Simple Package Download Statistics From CRAN", "topics": [ "packageDownloadStat" ] }, { "page": "pairsAsPropensMatr", "title": "Convert Pairs of Node-Names to Non-Oriented Propensity Matrix", "topics": [ "pairsAsPropensMatr" ] }, { "page": "partialDist", "title": "Partial distance matrix (focus on closest)", "topics": [ "partialDist" ] }, { "page": "partUnlist", "title": "Partial unlist of lists of lists", "topics": [ "partUnlist" ] }, { "page": "pasteC", "title": "Advanced paste-collapse", "topics": [ "pasteC" ] }, { "page": "presenceFilt", "title": "Filter Lines Of Matrix For Max Number Of NAs", "topics": [ "presenceFilt" ] }, { "page": "presenceGrpFilt", "title": "Filter For Each Group Of Columns For Sufficient Data As Non-NA", "topics": [ "presenceGrpFilt" ] }, { "page": "protectSpecChar", "title": "Protect Special Characters", "topics": [ "protectSpecChar" ] }, { "page": "pVal2lfdr", "title": "Convert p-values to lfdr", "topics": [ "pVal2lfdr" ] }, { "page": "pwSeparatorList", "title": "Suggestions Of Collections Of Classical Separators For Pairwise Combinations", "topics": [ "pwSeparatorList" ] }, { "page": "randIndFx", "title": "Distance of categorical data (Jaccard, Rand and adjusted Rand index)", "topics": [ "randIndFx" ] }, { "page": "rankToContigTab", "title": "Contingenty tables for fit of ranking", "topics": [ "rankToContigTab" ] }, { "page": "ratioAllComb", "title": "Calculate all ratios between x and y", "topics": [ "ratioAllComb" ] }, { "page": "ratioToPpm", "title": "Convert ratio to ppm", "topics": [ "ratioToPpm" ] }, { "page": "readCsvBatch", "title": "Read batch of csv-files", "topics": [ "readCsvBatch" ] }, { "page": "readTabulatedBatch", "title": "Batch Reading Of Tabulated Text-Files", "topics": [ "readTabulatedBatch" ] }, { "page": "readVarColumns", "title": "Read Tabular Content Of Files With Variable Number Of Columns", "topics": [ "readVarColumns" ] }, { "page": "readXlsxBatch", "title": "Read Batch of Excel xlsx-Files", "topics": [ "readXlsxBatch" ] }, { "page": "reduceTable", "title": "Reduce table by aggregating smaller groups", "topics": [ "reduceTable" ] }, { "page": "regrBy1or2point", "title": "Rescaling According To Reference Data Using Linear Regression.", "topics": [ "regrBy1or2point" ] }, { "page": "regrMultBy1or2point", "title": "Rescaling Of Multiple Data-Sets According To Reference Data Using Regression", "topics": [ "regrMultBy1or2point" ] }, { "page": "renameColumns", "title": "Rename columns", "topics": [ "renameColumns" ] }, { "page": "reorgByCluNo", "title": "Reorganize matrix according to clustering-output", "topics": [ "reorgByCluNo" ] }, { "page": "replacePWseparator", "title": "Replace Separator In Vector Of Pairwise Group-Names This function allows identifying and substituting a separator used in a character vector concatenated of pairwise groups.", "topics": [ "replacePWseparator" ] }, { "page": "replicateStructure", "title": "Search and Select Groups of Replicates", "topics": [ "replicateStructure" ] }, { "page": "replNAbyLow", "title": "Replace NAs by low values", "topics": [ "replNAbyLow" ] }, { "page": "replPlateCV", "title": "CV of replicate plates (list of matrixes)", "topics": [ "replPlateCV" ] }, { "page": "rmDupl2colMatr", "title": "Remove Lines Of Matrix Redundant /Duplicated For 1st And 2nd Column", "topics": [ "rmDupl2colMatr" ] }, { "page": "rmEnumeratorName", "title": "Remove or rename enumerator tag/name (or remove entire enumerator) from tailing enumerators", "topics": [ "rmEnumeratorName" ] }, { "page": "rmOrphans", "title": "Remove or Reassign Orphan Indexes", "topics": [ "rmOrphans" ] }, { "page": "rmSharedWords", "title": "Trim/Remove Redundant Words", "topics": [ "rmSharedWords" ] }, { "page": "rnormW", "title": "Normal random number generation with close fit to expected mean and sd", "topics": [ "rnormW" ] }, { "page": "rowCVs", "title": "rowCVs", "topics": [ "rowCVs" ] }, { "page": "rowGrpCV", "title": "Row group CV", "topics": [ "rowGrpCV" ] }, { "page": "rowGrpMeans", "title": "Row-Means With Destinction Of Groups (Of Columns, eg Groups Of Replicates)", "topics": [ "rowGrpMeans" ] }, { "page": "rowGrpNA", "title": "Count number of NAs per row and group of columns", "topics": [ "rowGrpNA" ] }, { "page": "rowGrpSds", "title": "Per line and per group sd-values", "topics": [ "rowGrpSds" ] }, { "page": "rowGrpSums", "title": "rowSums with destinction of groups (of columns, eg groups of replicates)", "topics": [ "rowGrpSums" ] }, { "page": "rowMedSds", "title": "Estimate sd Of Median For Each Row By Bootstrap", "topics": [ "rowMedSds" ] }, { "page": "rowNormalize", "title": "Row Normalize", "topics": [ "rowNormalize" ] }, { "page": "rowSds", "title": "sd for each row (fast execution)", "topics": [ "rowSds" ] }, { "page": "rowSEMs", "title": "SEM for each row", "topics": [ "rowSEMs" ] }, { "page": "sampNoDeMArrayLM", "title": "Locate Sample Index From Index Or Name Of Pair-Wise Comparisons In List Or MArrayLM-Object", "topics": [ "sampNoDeMArrayLM" ] }, { "page": "scaleXY", "title": "Scale data to given minimum and maxiumum", "topics": [ "scaleXY" ] }, { "page": "searchDataPairs", "title": "Search duplicated data over multiple columns, ie pairs of data", "topics": [ "searchDataPairs" ] }, { "page": "searchLinesAtGivenSlope", "title": "Search Points Forming Lines At Given Slope", "topics": [ "searchLinesAtGivenSlope" ] }, { "page": "simpleFragFig", "title": "Simple figure showing line from start- to end-sites of edges (or fragments) defined by their start- and end-sites 'simpleFragFig' draws figure showing start- and end-sites of edges (or fragments)", "topics": [ "simpleFragFig" ] }, { "page": "singleLineAnova", "title": "2-factorial Anova on single line of data", "topics": [ "singleLineAnova" ] }, { "page": "sortBy2CategorAnd1IntCol", "title": "Sort matrix by two categorical and one integer columns", "topics": [ "sortBy2CategorAnd1IntCol" ] }, { "page": "sortByNRepeated", "title": "Make a list of common occurances sorted by number of repeats", "topics": [ "sortByNRepeated" ] }, { "page": "stableMode", "title": "Estimate Mode (Most Frequent Value)", "topics": [ "stableMode" ] }, { "page": "standardW", "title": "Standardize (scale) data", "topics": [ "standardW" ] }, { "page": "stdErrMedBoot", "title": "Standard Eror Of Median by Boot-Strap", "topics": [ "stdErrMedBoot" ] }, { "page": "summarizeCols", "title": "Summarize columns (as median,mean,min,last or other methods)", "topics": [ "summarizeCols" ] }, { "page": "sumNAperGroup", "title": "Count number of NAs per sub-set of columns", "topics": [ "sumNAperGroup" ] }, { "page": "sysDate", "title": "System-date (compressed format)", "topics": [ "sysDate" ] }, { "page": "tableToPlot", "title": "Print matrix-content as plot", "topics": [ "tableToPlot" ] }, { "page": "test2factLimma", "title": "2-Factorial Limma-Style t-Test", "topics": [ "test2factLimma" ] }, { "page": "top3mean", "title": "Mean Of 3 Highest Values", "topics": [ "top3mean" ] }, { "page": "transpGraySca", "title": "Make single vector gray-gradient", "topics": [ "transpGraySca" ] }, { "page": "treatTxtDuplicates", "title": "Locate duplicates in text and make non-redundant", "topics": [ "treatTxtDuplicates" ] }, { "page": "triCoord", "title": "Pairwise x,y Combinations", "topics": [ "triCoord" ] }, { "page": "trimmedMean", "title": "Trimmed Mean", "topics": [ "trimmedMean" ] }, { "page": "trimRedundText", "title": "Trim redundant text", "topics": [ "trimRedundText" ] }, { "page": "tTestAllVal", "title": "t.test on all individual values against all other values", "topics": [ "tTestAllVal" ] }, { "page": "unifyEnumerator", "title": "Unify Enumerators", "topics": [ "unifyEnumerator" ] }, { "page": "uniqCountReport", "title": "Report number of unique and redundant elements (optional figure)", "topics": [ "uniqCountReport" ] }, { "page": "upperMaCoord", "title": "(upper) pairwise x,y combinations", "topics": [ "upperMaCoord" ] }, { "page": "withinRefRange", "title": "Check For Values Within Range Of Reference", "topics": [ "withinRefRange" ] }, { "page": "writeCsv", "title": "Write (And Convert) Csv Files", "topics": [ "writeCsv" ] }, { "page": "XYToDiffPpm", "title": "Express difference as ppm", "topics": [ "XYToDiffPpm" ] } ], "_rundeps": [ "MASS" ], "_vignettes": [ { "source": "wrMiscVignette1.Rmd", "filename": "wrMiscVignette1.html", "title": "Getting started with wrMisc", "author": "Wolfgang Raffelsberger", "engine": "knitr::rmarkdown", "headings": [ "Introduction", "Dependencies and Compilation", "Installation And Loading", "Speed Optimized Functions In The Package wrMisc", "Assessing Basic Information About Variability (for matrix)", "Data Organized In (Sub-)Groups As Sets Of Columns", "Counting Number Of NAs Per Row And Group Of Columns", "Fast NA-omit For Very Large Objects", "Minimum Distance/Difference Between Values", "Working With Lists (And Lists Of Lists)", "Partial unlist", "Appending/Combining Lists", "rbind On Lists", "cbind On Lists", "Merge Multiple Matrices From List", "Fuse Content Of List-Elements With Redundant (Duplicated) Names", "Filtering Lines And/Or Columns For All List-Elements Of Same Size", "Replacements In List", "Organize Values Into list and Sort By Names", "Batch-filter List-Elements", "Transform Columns Of Matrix To List Of Vectors", "Working With Arrays", "CV (Coefficient Of Variance) With Arrays", "Slice 3-dim Array In List Of Matrixes (Or Arrays)", "Working With Redundant Data", "Identify What Is Repeated (and Where Repeated Do Occur)", "Correct Vector To Unique (While Maintaining The Original Vector Length)", "Mark Any Duplicated (ie Ambiguous) Elements by Changing Their Names (and Separate from Unqiue)", "Compare Multiple Vectors And Sort By Number Of Common/Repeated Values/Words", "Combine Multiple Matrixes Where Some Column-Names Are The Same", "Filter Matrix To Keep Only First Of Repeated Lines", "Filter To Unique Column-Content Of Matrix, Add Counter And Concatenated Information", "Get First Of Repeated By Column", "Transform (ambigous) Matrix To Non-ambiguous Matrix (In Respect To Given Column)", "Combine Replicates From List To Matrix", "Combine Redundant Lines From List with (Multiple) Matrix According to Reference", "Non-redundant Lines Of Matrix", "Filter For Unique Elements /2", "Make Non-redundant Matrix", "Example : Summarize table for longest of transcripts", "Combine/Reduce Redundant Lines Based On Specified Column", "Convert Matrix (eg With Redundant) Row-Names To data.frame", "Find And Combine Points Located Very Close In X/Y Space", "Bin And Summarize Values According To Their Names", "Regrouping Simultaneaously by Two Factors", "Batch Replacing Of Values Or Character-Strings", "Multi-to-multi Matching Of (Concatenated) Terms", "Comparing Global Patterns", "Search For Similar (Numeric) Values", "Find Similar Numeric Values Of Two Columns Of A Matrix", "Find Similar Numeric Values From Two Vectors/Matrixes", "Fuse Previously Identified Pairs To 'Clusters'", "Eliminate Close (Overlapping) Points (In Bivariate x & y Space)", "Mode Of (Continuous) Data", "Most Frequently Occuring Value (traditional mode)", "Text-Manipulations", "Protect Special Characters", "Trimming Redundant Text", "Removing Redundant/Shared Words", "Extract Common Part Of Text", "Manipulating Enumerator-Extensions", "Remove/Modify Enumerators", "Unify Enumerators", "Find/Choose Column Most Likely Containing Sample-Names", "Find Common Unit", "Adjust Decimal Prefixes And Extact Numeric+Unit Part", "Merging Multiple Named Vectors To Matrix", "Match All Lines of Matrix To Reference Note", "Order Matrix According To Reference", "Value Matching With Option For Concatenated Terms", "Check for (Strict) Order", "Working With Regressions", "Best Starting Point For Linear Regressions (Start of linearity)", "High Throughput Testing For Linear Regressions", "Combinatorics Issues", "All Pairwise Ratios", "Count Frequency Of Terms Combined From Different Drawings (combineAsN)", "Import/Export", "Batch-Reading Of CSV Files", "Batch-Reading Of Tabulated Files", "Reading Incomplete Tables", "Converting Url For Reading Tabulated Data From GitHub", "Normalization", "Filter Lines Of Matrix To Reduce Content Of NAs", "Filter For Each Group Of Columns For Sufficient Data As Non-NA", "Filter As Separate Pairwise Groups Of Samples", "Cleaning Replicates", "The Function normalizeThis()", "Normalize By Rows", "Matrix Coordinates Of Values/Points According To Filtering", "Trimmed Mean", "Statistical Testing", "Normal Random Number Generation with Close Fit to Expected mean and sd", "Moderated Pair-Wise t-Test from limma", "Multiple Moderated Pair-Wise t-Tests From limma", "Choosing amongst multiple possible pairwise comparisons", "Transform p-values To Local False Discovery Rate (lfdr)", "Confindence Intervals (under Normal Distribution)", "Extract Groups Of Replicates From Pair-Wise Column-Names", "Extract Numeric Part Of Column-Names", "Automatic Determination Of Replicate Structure Based On Meta-Data", "Addressing Pairwise Comparisons", "Suggesting A Separator For Pairwise Combinations", "Identify The Separator Used In Concatenated Text", "Working With Clustering", "Prepare Data For Clustering", "Characterize Clustering Results", "Remove or Reassign Orphans", "Tree-Like Structures", "Filter Lists Of Connected Nodes, Extension Of Networks As 'Sandwich'", "Convert Collection Of Pairs Of Nodes To Propensity Matrix", "Characterize Individual Contribution Of Single Edges In Tree-Structures", "Count Same Start- And End- Sites Of Edges (Or Fragments)", "Support for Graphical Output", "Convenient Paste-Collapse", "Transform Numeric Values to Color-Gradient", "Assign New Transparency To Given Colors", "Print Matrix-Content As Plot", "Other Convenience Functions", "Writing Compact Dates (more options ...)", "Acknowledgements", "Session-Info" ], "created": "2020-04-23 15:30:02", "modified": "2026-04-29 11:56:52", "commits": 35 } ], "_score": 4.389602641040325, "_indexed": true, "_nocasepkg": "wrmisc", "_universes": [ "wraff" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.0.2", "date": "2026-05-25T06:46:43.000Z", "distro": "noble", "commit": "eb2f7d0663afa382a21011f2bc6afc1367c3829e", "fileid": "49b5696f9df5d74d86e736597728338dc686fccebe8f10b2c38fa8fcc8d82b3c", "status": 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