# Analyze Experimental High-Throughput (Omics) Data

## Documentation for package ‘wrMisc’ version 1.9.0

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

## Help Pages

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