Man pages for wrMisc
Analyze Experimental High-Throughput (Omics) Data

addBeforFileExtensionAdd text before file-extension
adjBy2ptRegLinear rescaling of numeric vertor or matrix
appendNRAppend vectors or lists, without duplcating common elements
arrayCVCV of array
asSepListOrganize Data as Separate List-Entries
buildTreeConnect edges to from tree and extract all possible branches
cbindNRcbind to non-redundant
checkAvSdCheck how multiple groups of data separate or overlap based...
checkGrpOrderSEMCheck order of multiple groups including non-overlapping...
checkSimValueInSerCheck for similar values in series
checkStrictOrderCheck for strict (ascencing or descending) order
checkVectLengthCheck length of vector
cleanReplicatesReplace Most Distant Values by NA
closeMatchMatrixReorganize results of search for close (similar) values in...
coinPermTestCompare means of two vectors by permutation test
colMedSdsStandard error of median for each column by bootstrap
colorAccording2Transform numeric values to color-gradient
colSdssd for each column
combinatIntTablePlaning for making all multiplicative combinations
combineAsNCombine Vectors From List And Return Basic Count Statistics
combineByEitherFactorCreate factor-like column regrouping data regrouping...
combineOverlapInfoFind and combine points located very close in x/y space
combineRedBasedOnColCombine/reduce redundant lines based on specified column
combineReplFromListToMatrCombine replicates from list to matrix
combineSingleTGet all combinations with TRUE from each column
completeArrLstComplete list of arrays for same dimensions
confIntConfidence Interval To Given Alpha
contribToContigPerFragCharacterize individual contribution of single edges in...
conv01toColNaConvert matrix of integer to matrix of x-times repeated...
convColorToTranspAssign new transparency to given colors
convMatr2dfConvert matrix (eg with redundant) row-names to data.frame
convToNumConvert vector to numeric
coordOfFiltget coordinates of values/points in matrix according to...
correctToUniqueCorrect vector to unique
correctWinPathCorrect mixed slash and backslash in file path
countCloseToLimitsCount from two vectors number of values close within given...
countSameStartEndCount same start- and end- sites of edges (or fragments)
cutArrayInCluLikeCut 3-dim array in list of matrixes (or arrays) similar to...
cutAtMultSitesCut character-vector at multiple sites
cutToNgrpCut numeric vector to n groups (ie convert to factor)
diffCombinCompute matrix of differences for all pairwise combinations...
diffPPMDifference in ppm between numeric values
dot-addLetterWoLastAdd letter to all elements but not last
dot-allRatioMatr1to2Calculate ratios for each column to each column of...
dot-allRatiosSearch character-string and cut either before or after
dot-arrLstMeanSummarize along columns of multiple arrays in list
dot-arrLstSEMSummarize along columns of mult arrays in list
dot-asDF2Convert anything to data.frame
dot-breakInSerGet series of values after last discontinuity
dot-bringToCtrBring most extreme to center
dot-checkArgNaCheck argument names
dot-checkConsistentArrListCheck list of arrays for consistent dimensions of all arrays
dot-checkConvt2VectConvert to simple vector (similar to unlist)
dot-checkFactorCheck Factor
dot-checkFileNameExtensionscheckFileNameExtensions Function for checking file-names.
dot-checkLegendLocCheck argument for Location of legend
dot-checkLmConfIntCompare 'dat' to confindence interval of linare model 'lMod'...
dot-checkRegrArgumentsCheck regression arguments
dot-chooseGrpColAutomatic choice of colors
dot-combineListAnnotCombine annotation information from list of matrixes
dot-compareByDiffCompare by distance/difference
dot-compareByLogRatioCompare by log-ratio
dot-compareByPPMCompare by PPM
dot-complColsSearch (complementing) columns for best coverage of non-NA...
dot-composeCallNameCompose sequence of (function-)calls
dot-convertMatrToNumConvert numeric matrix to numeric
dot-convertNaConvert/standardize names of 'query' to standard names from...
dot-corDuplItemsByIncremAvoid duplicating items between 'curNa' and 'newNa' by...
dot-cutAtSearchSearch character-string and cut either before or after
dot-cutStrCut string to get all variants from given start with min and...
dot-datSlopeModel linear regression and optional plot
dot-extrNAneighbExtract NA-neighbour values
dot-extrNumHeadingCapExtract number(s) before capital character
dot-extrNumHeadingSepCharExtract numbers before separator followed by alphabetic...
dot-filterNetwFilter nodes & edges for extracting networks (main) This...
dot-filterSwFilter 3-dim array of numeric data (main)
dot-filtSizeFilter for size
dot-findBorderOverlapsFind overlap instances among range of values in lines
dot-firstMinGet first minimum
dot-fuse2ArrBy2ndDimfuse 2 instances of 3dim arr as mult cols in 3dim array
dot-getAmeanGet A value for each group of replicates
dot-getAmean2Get A value for each group of replicates based on comp
dot-getMvalue2Get M value for each group of replicates based on comp
dot-growTreeGrow tree
dot-insp1dimByClusteringSegment (1-dim vector) 'dat' into clusters
dot-inspectHeaderInspect 'matr' and check if 1st line can be used/converted as...
dot-keepCenter1dRefine/filter 'dat1' (1dim dataset, eg cluster) with aim of...
dot-keepFiniteColRemove all columns where all data are not finite
dot-mayBeNumCheck if vector may be numeric content
dot-medianSpecGrpRescale respective to specific group
dot-mergeMatricesMerge Multiple Matrices (main)
dot-minDiffind closest neighbour to numeric vector
dot-neigbDisDistances beteenw sorted points of 2-columns
dot-normalizeMain Normalization function
dot-normConstSlopeNormalize columns of 2dim matrix to common linear regression...
dot-offCenterReturn position of 'di' (numeric vector) which is most...
dot-pasteColsPaste-concatenate all columns of matrix
dot-plotCountPiePie plot for counting results
dot-plusLowerCapsAdd lower caps to character vector
dot-predResCalculate residues of (2-dim) linear model 'lMod'-prediction...
dot-raiseColLowestRaise all values close to lowest value
dot-removeColRemove columns indicated by col-number
dot-removeEmptyColSearch for (empty) columns conaining only entries defined in...
dot-replSpecCharReplace Special Characters
dot-retain1stPartTrim character string: keep only text before 'sep'
dot-rowGrpCVrow group CV (main)
dot-rowGrpMeansrow group mean (main)
dot-rowGrpSdsrow group sd (main)
dot-rowGrpSumsrow group rowSums per group (main)
dot-rowNormRow-normalization procedure on matrix or data.frame 'dat'
dot-rowNormFactObtain normalization factor (main)
dot-scale01Scale between 0 and 1 (main)
dot-scaleSpecGrpRescale respective to specific group
dot-scaleXYScale between min and max value (main)
dot-seqCutStrCut string to get all variants from given start with min...
dot-setLowestToSet lowest value to given value
dot-sortMidChoose most frequent or middle of sorted vector
dot-stackArrayReorganize array by reducing dimension 'byDim' (similar to...
dot-summarizeColsSummarize columns of matrix (or data.frame) 'x' using apply...
dot-trimFromEndTrim from end
dot-trimFromStartTrim from start
dot-trimLeftTrim from Left
dot-trimRightTrim from right
dot-uniqueWNameCheck regression arguments
dot-vector2MatrConvert numeric vector to matrix
elimCloseCoordEliminate close (overlapping) points (in x & y space)
equLenNumberEqual character-length number
exclExtrValuesExclude extreme values (based on distance to mean)
exponNormalizeNormalize by adjusting exponent
extr1chanExtract just one series, ie channel, of list of arrays
extractLast2numericPartsExtract last two numeric parts from character vector
extrColsDeXFlexible extraction of columns
extrNumericFromMatrExtract numeric part of matrix or data.frame
extrSpcTextExtract specific text
filt3dimArrFilter three-dimensional array of numeric data
filterLiColDeListFilter lines(rows) and/or columns from all suitable elements...
filterListFilter for unique elements
filterNetwFilter nodes & edges for extracting networks This function...
filtSizeUniqFilter for unique elements
findCloseMatchFind close numeric values between two vectors
findRepeatedFind repeated elements
findSimilFrom2setsFind similar numeric values from two vectors/matrixes
findUsableGroupRangeSelect groups within given range
firstLineOfDatFilter matrix to keep only first of repeated lines
firstOfRepeatedFind first of repeated elements
firstOfRepLinesReduce to first occurance of repeated lines
fuseAnnotMatrFuse annotation matrix to initial matrix
fuseCommonListElemFuse content of list-elements with redundant (duplicated)...
fusePairsFuse pairs to generate cluster-names
get1stOfRepeatedByColGet first of repeated by column
getValuesByUniquePrint matrix-content as plot
gitDataUrlConvert ulr-name for reading in raw-mode
htmlSpecCharConvHtml special character conversion
keepCommonTextExtract Longest Common Text Out Of Character Vector
levIndexTransform (factor) levels into index
linModelSelectTest multiple starting levels for linear regression model,...
linRegrParamAndPValFit linear regression, return parameters and p-values
listBatchReplaceReplacements in list
listGroupsByNamesOrganize values into list and sort by names
lmSelCluRun lm on segmented data (from clustering)
lrbindrbind on lists
makeMAListMake MA-List object
makeNRedMatrMake non-redundant matrix
matchMatrixLinesToRefMatch All Lines of Matrix To Reference Note
matchNamesWithReversePartsValue Matching with optional reversing of sub-parts of...
matchSampToPairwMatch names to concatenated pairs of names
matr2listTransform columns of matrix to list of vectors
mergeMatricesMerge Multiple Matrices
mergeMatrixListMerge Multiple Matrices from List
mergeSelColMerge selected columns out of 2 matrix or data.frames
mergeVectorsMerge Named Vectors
mergeW2Extended version of merge for multiple objects (even without...
minDiffMinimum distance/difference between values
moderTest2grpModerated pair-wise t-test from limma
moderTestXgrpMultiple moderated pair-wise t-tests from limma
multiCharReplaceMultiple replacement of entire character elements in simple...
multiMatchSimple Multi-to-Multi Matching of (Concatenated) Terms
naOmitFast na.omit
nFragmentsNumber of fragments after cut at specific character(s) within...
nFragments0Number of fragments after cut at specific character(s)
nNonNumCharCount number of non-numeric characters
nonAmbiguousMatTransform matrix to non-ambiguous matrix (in respect to given...
nonAmbiguousNummake numeric vector non-ambiguous (ie unique)
nonredDataFrameFilter for unique elements
nonRedundLinesNon-redundant lines of matrix
normalizeThisNormalize data in various modes
numPairDeColNamesExtract pair of numeric values from vector or column-names
orderMatrToRefOrder Lines of Matrix According to Reference (Character)...
organizeAsListOfRepl(re)organize data of (3-dim) array as list of replicates
packageDownloadStatSimple Package Download Statistics from CRAN
pairsAsPropensMatrConvert Pairs of Node-Names to Non-Oriented Propensity Matrix
partialDistPartial distance matrix (focus on closest)
partUnlistPartial unlist of lists of lists
pasteCAdvanced paste-collapse
presenceFiltFilter lines of matrix for max number of NAs
presenceGrpFiltFilter for each group of columns for sufficient data as...
protectSpecCharProtect Special Characters
pVal2lfdrConvert p-values to lfdr
randIndFxDistance of categorical data (Jaccard, Rand and adjusted Rand...
rankToContigTabContingenty tables for fit of ranking
ratioAllCombCalculate all ratios between x and y
ratioToPpmConvert ratio to ppm
readCsvBatchRead batch of csv-files
readTabulatedBatchBatch reading of Tabulated Text-Files
readVarColumnsRead tabular content of files with variable number of columns
readXlsxBatchRead Batch of Excel xlsx-Files
reduceTableReduce table by aggregating smaller groups
regrBy1or2pointRescaling according to reference data using linear...
regrMultBy1or2pointRescaling of multiple data-sets according to reference data...
renameColumnsRename columns
reorgByCluNoReorganize matrix according to clustering-output
replicateStructureSearch and Select Groups of Replicates
replNAbyLowReplace NAs by low values
replPlateCVCV of replicate plates (list of matrixes)
rmDupl2colMatrRemove lines of matrix redundant /duplicated for 1st and 2nd...
rmEnumeratorNameRemove or rename enumerator tag/name (or remove entire...
rnormWNormal random number generation with close fit to expected...
rowGrpCVRow group CV
rowGrpMeansrowMeans with destinction of groups (of columns, eg groups of...
rowGrpNACount number of NAs per row and group of columns
rowGrpSdsPer line and per group sd-values
rowGrpSumsrowSums with destinction of groups (of columns, eg groups of...
rowMedSdssd of median for each row by bootstrap
rowNormalizeRow Normalize
rowSdssd for each row (fast execution)
rowSEMsSEM for each row
sampNoDeMArrayLMLocate Sample Index From Index or Name Of Pair-Wise...
scaleXYScale data to given minimum and maxiumum
searchDataPairsSearch duplicated data over multiple columns, ie pairs of...
searchLinesAtGivenSlopeSearch points forming lines at given slope
simpleFragFigSimple figure showing line from start- to end-sites of edges...
singleLineAnova2-factorial Anova on single line of data
sortBy2CategorAnd1IntColSort matrix by two categorical and one integer columns
sortByNRepeatedMake a list of common occurances sorted by number of repeats
stableModeEstimate mode (most frequent value)
standardWStandardize (scale) data
stdErrMedBootStandard eror of median by boot-strap
summarizeColsSummarize columns (as median,mean,min,last or other methods)
sumNAperGroupCount number of NAs per sub-set of columns
sysDateSystem-date (compressed format)
tableToPlotPrint matrix-content as plot
test2factLimma2-factorial limma-style t-test
transpGrayScaMake single vector gray-gradient
treatTxtDuplicatesLocate duplicates in text and make non-redundant
triCoordPairwise x,y combinations
trimRedundTextTrim redundant text
tTestAllValt.test on all individual values against all other values
unifyEnumeratorUnify Enumerators
uniqCountReportReport number of unique and redundant elements (optional...
upperMaCoord(upper) pairwise x,y combinations
withinRefRangeCheck for values within range of reference
writeCsvWrite (and convert) csv files
XYToDiffPpmExpress difference as ppm
wrMisc documentation built on March 31, 2023, 5:56 p.m.