Analyze Experimental High-Throughput (Omics) Data

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Documentation for package ‘wrMisc’ version 1.14.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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

-- A --

addBeforFileExtension	Add text before file-extension
adjBy2ptReg	Linear rescaling of numeric vertor or matrix
adjustUnitPrefix	Adjust Value With Different Decimal Prefixes To Single Prefix Plus Unit
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
checkFilePath	Check If File Is Available For Reading
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
combineAsN	Combine Vectors From List And Return Basic Count Statistics
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
combineRedundLinesInList	Combine Redundant Lines In List
combineRedundLinesInListAcRef	Combine Redundant Lines In List, Deprecated
combineReplFromListToMatr	Combine replicates from list to matrix
combineSingleT	Get all combinations with TRUE from each column
completeArrLst	Complete list of arrays for same dimensions
concatMatch	Value Matching With Option For Concatenated Terms
confInt	Confidence Interval To Given Alpha
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 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

-- K --

keepCommonText

Extract Longest Common Text Out Of Character Vector

-- 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
matchMatrixLinesToRef	Match All Lines of Matrix To Reference Note
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
mergeMatrices	Merge Multiple Matrices
mergeMatrixList	Merge Multiple Matrices from List
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 --

orderMatrToRef	Order Lines of Matrix According to Reference (Character) Vector
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
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
presenceGrpFilt	Filter for each group of columns for sufficient data as non-NA
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
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
rmEnumeratorName	Remove or rename enumerator tag/name (or remove entire enumerator) from tailing enumerators
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
rowGrpSums	rowSums with destinction of groups (of columns, eg groups of replicates)
rowMedSds	sd of median for each row by bootstrap
rowNormalize	Row Normalize
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
sortByNRepeated	Make a list of common occurances sorted by number of repeats
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 --

unifyEnumerator	Unify Enumerators
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

-- misc --

.addLetterWoLast	Add letter to all elements but not last
.allRatioMatr1to2	Calculate ratios for each column to each column of reference-matrix
.allRatios	Search character-string and cut either before or after
.arrLstMean	Summarize along columns of multiple arrays in list
.arrLstSEM	Summarize along columns of mult arrays in list
.asDF2	Convert anything to data.frame
.breakInSer	Get series of values after last discontinuity
.bringToCtr	Bring most extreme to center
.checkArgNa	Check argument names
.checkConsistentArrList	Check list of arrays for consistent dimensions of all arrays
.checkConvt2Vect	Convert to simple vector (similar to unlist)
.checkFactor	Check Factor
.checkFileNameExtensions	checkFileNameExtensions Function for checking file-names.
.checkLegendLoc	Check argument for Location of legend
.checkLmConfInt	Compare 'dat' to confindence interval of linare model 'lMod' (eg from lm())
.checkRegrArguments	Check regression arguments
.chooseGrpCol	Automatic choice of colors
.combineListAnnot	Combine annotation information from list of matrixes
.compareByDiff	Compare by distance/difference
.compareByLogRatio	Compare by log-ratio
.compareByPPM	Compare by PPM
.complCols	Search (complementing) columns for best coverage of non-NA data for rowNormalization (main)
.composeCallName	Compose sequence of (function-)calls
.convertMatrToNum	Convert numeric matrix to numeric
.convertNa	Convert/standardize names of 'query' to standard names from 'ref'
.corDuplItemsByIncrem	Avoid duplicating items between 'curNa' and 'newNa' by incrementing digits after 'extPref' (in newNa)
.cutAtSearch	Search character-string and cut either before or after
.cutStr	Cut string to get all variants from given start with min and max length
.datSlope	Model linear regression and optional plot
.extrNAneighb	Extract NA-neighbour values
.extrNumHeadingCap	Extract number(s) before capital character
.extrNumHeadingSepChar	Extract numbers before separator followed by alphabetic character
.filterNetw	Filter nodes & edges for extracting networks (main) 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.
.filterSw	Filter 3-dim array of numeric data (main)
.filtSize	Filter for size
.findBorderOverlaps	Find overlap instances among range of values in lines
.firstMin	Get first minimum
.fuse2ArrBy2ndDim	fuse 2 instances of 3dim arr as mult cols in 3dim array
.getAmean	Get A value for each group of replicates
.getAmean2	Get A value for each group of replicates based on comp
.getMvalue2	Get M value for each group of replicates based on comp
.growTree	Grow tree
.insp1dimByClustering	Segment (1-dim vector) 'dat' into clusters
.inspectHeader	Inspect 'matr' and check if 1st line can be used/converted as header
.keepCenter1d	Refine/filter 'dat1' (1dim dataset, eg cluster) with aim of keeping center of data
.keepFiniteCol	Remove all columns where all data are not finite
.mayBeNum	Check if vector may be numeric content
.medianSpecGrp	Rescale respective to specific group
.mergeMatrices	Merge Multiple Matrices (main)
.minDif	find closest neighbour to numeric vector
.neigbDis	Distances beteenw sorted points of 2-columns
.normalize	Main Normalization function
.normConstSlope	Normalize columns of 2dim matrix to common linear regression fit
.offCenter	Return position of 'di' (numeric vector) which is most excentric (distant to 0), starts with NAs as most excentric
.pasteCols	Paste-concatenate all columns of matrix
.plotCountPie	Pie plot for counting results
.plusLowerCaps	Add lower caps to character vector
.predRes	Calculate residues of (2-dim) linear model 'lMod'-prediction of/for 'dat'
.raiseColLowest	Raise all values close to lowest value
.removeCol	Remove columns indicated by col-number
.removeEmptyCol	Search for (empty) columns conaining only entries defined in 'searchFields' and remove such columns
.replSpecChar	Replace Special Characters
.retain1stPart	Trim character string: keep only text before 'sep'
.rowGrpCV	row group CV (main)
.rowGrpMeans	row group mean (main)
.rowGrpSds	row group sd (main)
.rowGrpSums	row group rowSums per group (main)
.rowNorm	Row-normalization procedure on matrix or data.frame 'dat'
.rowNormFact	Obtain normalization factor (main)
.scale01	Scale between 0 and 1 (main)
.scaleSpecGrp	Rescale respective to specific group
.scaleXY	Scale between min and max value (main)
.seqCutStr	Cut string to get all variants from given start with min length, depreciated
.setLowestTo	Set lowest value to given value
.sortMid	Choose most frequent or middle of sorted vector
.stackArray	Reorganize array by reducing dimension 'byDim' (similar to stack() for data-frames)
.summarizeCols	Summarize columns of matrix (or data.frame) 'x' using apply (main)
.trimFromEnd	Trim from end
.trimFromStart	Trim from start
.trimLeft	Trim from Left
.trimRight	Trim from right
.uniqueWName	Check regression arguments
.vector2Matr	Convert numeric vector to matrix