# Analyze Experimental High-Throughput (Omics) Data

## Documentation for package ‘wrMisc’ version 2.1.0

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

## Help Pages

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

## -- A --

addBeforeFileExtension | Add Text Before File-Extension
addBeforFileExtension | Add Text Before File-Extension
adjBy2ptReg | Adjust Values By Two-Point Regression
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 --

blockNormalize | Normalize Blockwise Two Or Three Datasets
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 | Verify File-name If Existing (in specified path), If Has Proper Extension Or Select Files With Proper Extension From Given Path
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
checkUnitPrefix | Check For Common Unit-Name in Text
checkVectLength | Check length of vector
chooseGroupNames | Choose Column Most Likely For Sample-Names
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
colCVs | rowCVs
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
convPairwiseSetup | Check Comparison-Choice
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 One 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 UniqueElements
findCloseMatch | Find Close Numeric Values Between Two Vectors
findHeadAndTail | Find Group-Names In Pairwise Combined And Isolate Separator
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
getPairwiseSetup | Extract Pairwise Testing Setup
getPWseparator | 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.
getValuesByUnique | Print matrix-content as plot
gitDataUrl | Convert GitHub Url-Name For Reading In Raw-Mode

## -- H --

htmlSpecCharConv | Html Special Character Conversion

## -- I --

indexGroupsFromPW | Index Names Of Groups From Vector Of Concatenated Pairwise Group-Names

## -- 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 Pairwise t-test From Limma
moderTestXgrp | Multiple Moderated Pairwise 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
pwSeparatorList | Suggestions Of Collections Of Classical Separators For Pairwise Combinations

## -- 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
replacePWseparator | 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.
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
rmOrphans | Remove or Reassign Orphan Indexes
rmSharedWords | Trim/Remove Redundant Words
rnormW | Normal random number generation with close fit to expected mean and sd
rowCVs | rowCVs
rowGrpCV | Row group CV
rowGrpMeans | Row-Means 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 | Estimate 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 | Rescale Data To Given Minimum- And Maxiumum- Values
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
top3mean | Mean Of 3 Highest Values
transpGraySca | Make single vector gray-gradient
treatTxtDuplicates | Locate duplicates in text and make non-redundant
triCoord | Pairwise x,y Combinations
trimmedMean | Trimmed Mean
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

## -- V --

vectorDistAngle | Vector Distance and Angle
volcanoFilter | Filter Statistical Testing Results in Volcano-Plot Like Fashion This function allows filtering statistical testing results combined with M-values (log2 fold-change) and other filtering criteria. All suitable values can be extracted from objects created from package wrProteo (and limma) may get used automatically. The outcome can be used for Volcano-plots or exporting tables.

## -- 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 | Check File Name Extensions 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
.doubleExt | Return File-name Extensions Including Double Extensions (eg txt.gz)
.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
.getPWseparator | Find Separator In Vector Of Pairwise Group-Names This function allows identifing separator used when pairwise groups are presented.
.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 2-dim Matrix To Common Linear Regression Fit
.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 (main)
.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 (Deprecated)
.trimFromStart | Trim from start (Deprecated)
.trimLeft | Trim From Left Side
.trimRight | Trim From Right Side
.uniqueWName | Check regression arguments
.vector2Matr | Convert numeric vector to matrix