# Analyze Experimental High-Throughput (Omics) Data

## Documentation for package ‘wrMisc’ version 1.13.0

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

## Help Pages

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
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