Analyze Experimental High-Throughput (Omics) Data


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Documentation for package ‘wrMisc’ version 1.9.0

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A B C D E F G H L M N O P R S T U W X

-- A --

addBeforFileExtension Add text before file-extension
adjBy2ptReg Linear rescaling of numeric vertor or matrix
appendNR Append vectors or lists, without duplcating common elements
arrayCV CV of array
asSepList Organize data as separate list-entries

-- B --

buildTree Connect edges to from tree and extract all possible branches

-- C --

cbindNR cbind to non-redundant
checkAvSd Check how multiple groups of data separate or overlap based on mean +/- sd
checkGrpOrder checkGrpOrder
checkGrpOrderSEM Check order of multiple groups including non-overlapping SEM-margins
checkSimValueInSer Check for similar values in series
checkStrictOrder Check for strict (ascencing or descending) order
checkVectLength Check length of vector
cleanReplicates Replace most distant values by NA
closeMatchMatrix Reorganize results of search for close (similar) values in matrix-view
coinPermTest Compare means of two vectors by permutation test
colMedSds Standard error of median for each column by bootstrap
colorAccording2 Transform numeric values to color-gradient
colSds sd for each column
combinatIntTable Planing for making all multiplicative combinations
combineByEitherFactor Create factor-like column regrouping data regrouping simultaneaously by two factors
combineOverlapInfo Find and combine points located very close in x/y space
combineRedBasedOnCol Combine/reduce redundant lines based on specified column
combineReplFromListToMatr Combine replicates from list to matrix
combineSingleT Get all combinations with TRUE from each column
completeArrLst Complete list of arrays for same dimensions
contribToContigPerFrag Characterize individual contribution of single edges in tree-structures
conv01toColNa Convert matrix of integer to matrix of x-times repeated column-names
convColorToTransp Assign new transparency to given colors
convMatr2df Convert matrix (eg with redundant) row-names to data.frame
convToNum Convert vector to numeric
coordOfFilt get coordinates of values/points in matrix according to filtering condition
correctToUnique Correct vector to unique
correctWinPath Correct mixed slash and backslash in file path
countCloseToLimits Count from two vectors number of values close within given limits
countSameStartEnd Count same start- and end- sites of edges (or fragments)
cutArrayInCluLike Cut 3-dim array in list of matrixes (or arrays) similar to organizing into clusters
cutAtMultSites Cut character-vector at multiple sites
cutToNgrp Cut numeric vector to n groups (ie convert to factor)

-- D --

diffCombin Compute matrix of differences for all pairwise combinations of numeric vector
diffPPM Difference in ppm between numeric values

-- E --

elimCloseCoord Eliminate close (overlapping) points (in x & y space)
equLenNumber Equal character-length number
exclExtrValues Exclude extreme values (based on distance to mean)
exponNormalize Normalize by adjusting exponent
extr1chan Extract just one series, ie channel, of list of arrays
extractLast2numericParts Extract last two numeric parts from character vector
extrColsDeX Flexible extraction of columns
extrNumericFromMatr Extract numeric part of matrix or data.frame
extrSpcText Extract specific text

-- F --

filt3dimArr Filter a three-dimensional array of numeric data
filterLiColDeList Filter lines(rows) and/or columns from all suitable elements of list
filterList Filter for unique elements
filterNetw 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.
filtSizeUniq Filter for unique elements
findCloseMatch Find close numeric values between two vectors
findRepeated Find repeated elements
findSimilFrom2sets Find similar numeric values from two vectors/matrixes
findUsableGroupRange Select groups within given range
firstLineOfDat Filter matrix to keep only first of repeated lines
firstOfRepeated Find first of repeated elements
firstOfRepLines Reduce to first occurance of repeated lines
fuseAnnotMatr Fuse annotation matrix to initial matrix
fuseCommonListElem Fuse content of list-elements with redundant (duplicated) names
fusePairs Fuse pairs to generate cluster-names

-- G --

get1stOfRepeatedByCol Get first of repeated by column
getValuesByUnique Print matrix-content as plot
gitDataUrl Convert ulr-name for reading in raw-mode

-- H --

htmlSpecCharConv Html special character conversion

-- L --

levIndex Transform (factor) levels into index
linModelSelect Test multiple starting levels for linear regression model, select best and plot
linRegrParamAndPVal Fit linear regression, return parameters and p-values
listBatchReplace Replacements in list
listGroupsByNames Organize values into list and sort by names
lmSelClu Run lm on segmented data (from clustering)
lrbind rbind on lists

-- M --

makeMAList Make MA-List object
makeNRedMatr Make non-redundant matrix
matchNamesWithReverseParts Value Matching with optional reversing of sub-parts of non-matching elements
matchSampToPairw Match names to concatenated pairs of names
matr2list Transform columns of matrix to list of vectors
mergeSelCol Merge selected columns out of 2 matrix or data.frames
mergeSelCol3 mergeSelCol3
mergeVectors Merge Named Vectors
mergeW2 Extended version of merge for multiple objects (even without rownames)
minDiff Minimum distance/difference between values
moderTest2grp Moderated pair-wise t-test from limma
moderTestXgrp Multiple moderated pair-wise t-tests from limma
multiCharReplace Multiple replacement of entire character elements in simple vector, matrix or data.frame
multiMatch Simple Multi-to-Multi Matching of (Concatenated) Terms

-- N --

naOmit Fast na.omit
nFragments Number of fragments after cut at specific character(s) within size-range
nFragments0 Number of fragments after cut at specific character(s)
nNonNumChar Count number of non-numeric characters
nonAmbiguousMat Transform matrix to non-ambiguous matrix (in respect to given column)
nonAmbiguousNum make numeric vector non-ambiguous (ie unique)
nonredDataFrame Filter for unique elements
nonRedundLines Non-redundant lines of matrix
normalizeThis Normalize data in various modes
numPairDeColNames Extract pair of numeric values from vector or column-names

-- O --

organizeAsListOfRepl (re)organize data of (3-dim) array as list of replicates

-- P --

packageDownloadStat Simple Package Download Statistics from CRAN
pairsAsPropensMatr Convert pairs of node-names to non-oriented propensity matrix Numerous network query tools produce a listing of pairs of nodes (with one pair of nodes per line). Using this function such a matrix (or data.frame) can be combined to this more comprehensive view as propensity-matrix. Note, this has been primarily developed for undireted interaction networks, the resulting propensity-matrix does not show any orientation any more. In a number of applications (eg in protein-protein interaction networks, PPI) the resulting matrix may be rather sparse.
partialDist Partial distance matrix (focus on closest)
partUnlist Partial unlist of lists of lists
pasteC Advanced paste-collapse
presenceFilt Filter lines of matrix for max number of NAs
protectSpecChar Protect Special Characters
pVal2lfdr Convert p-values to lfdr

-- R --

randIndFx Distance of categorical data (Jaccard,Rand and adjusted Rand index)
rankToContigTab Contingenty tables for fit of ranking
ratioAllComb Calculate all ratios between x and y
ratioToPpm Convert ratio to ppm
readCsvBatch Read batch of csv-files
readTabulatedBatch Batch reading of tabulated (text-) files This function allows batch reading of multiple tabulated text files. The files can be designed specifically, alternatively all files from a given directory can be read. If package data.table is available, fast reading of files will be performed using the function 'fread'.
readVarColumns Read tabular content of files with variable number of columns
readXlsxBatch Read batch of Excel xlsx-files
reduceTable Reduce table by aggregating smaller groups
regrBy1or2point Rescaling according to reference data using linear regression.
regrMultBy1or2point Rescaling of multiple data-sets according to reference data using regression
renameColumns Rename columns
reorgByCluNo Reorganize matrix according to clustering-output
replicateStructure Search and Select Groups of Replicates
replNAbyLow Replace NAs by low values
replPlateCV CV of replicate plates (list of matrixes)
rmDupl2colMatr Remove lines of matrix redundant /duplicated for 1st and 2nd column
rnormW Normal random number generation with close fit to expected mean and sd
rowCVs rowCVs
rowGrpCV row group CV
rowGrpMeans rowMeans with destinction of groups (of columns, eg groups of replicates)
rowGrpNA Count number of NAs per row and group of columns
rowGrpSds Per line and per group sd-values
rowMedSds sd of median for each row by bootstrap
rowSds sd for each row (fast execution)
rowSEMs SEM for each row

-- S --

sampNoDeMArrayLM Locate sample index from index or name of pair-wise comparisons in list or MArrayLM-object
scaleXY Scale data to given minimum and maxiumum
searchDataPairs Search duplicated data over multiple columns, ie pairs of data
searchLinesAtGivenSlope Search points forming lines at given slope
simpleFragFig 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)
singleLineAnova 2-factorial Anova on single line of data
sortBy2CategorAnd1IntCol Sort matrix by two categorical and one integer columns
stableMode Estimate mode (most frequent value)
standardW Standardize (scale) data
stdErrMedBoot Standard eror of median by boot-strap
summarizeCols Summarize columns (as median,mean,min,last or other methods)
sumNAperGroup Count number of NAs per sub-set of columns
sysDate System-date (compressed format)

-- T --

tableToPlot Print matrix-content as plot
test2factLimma 2-factorial limma-style t-test
transpGraySca Make single vector gray-gradient
treatTxtDuplicates Locate duplicates in text and make non-redundant
triCoord Pairwise x,y combinations
trimRedundText Trim redundant text
tTestAllVal t.test on all individual values against all other values

-- U --

uniqCountReport Report number of unique and redundant elements (optional figure)
upperMaCoord (upper) pairwise x,y combinations

-- W --

withinRefRange Check for values within range of reference
writeCsv Write (and convert) csv files

-- X --

XYToDiffPpm Express difference as ppm