.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
.filtSize               Filter for size
.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)
.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
.normConstSlope         Normalize Columns Of 2-dim Matrix To Common
                        Linear Regression Fit
.normalize              Main Normalization function
.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
XYToDiffPpm             Express difference as ppm
addBeforFileExtension   Add Text Before File-Extension
addBeforeFileExtension
                        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
blockNormalize          Normalize Blockwise Two Or Three Datasets
buildTree               Connect edges to from tree and extract all
                        possible branches
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           Check Order Of Groups
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
colSds                  sd for each column
colorAccording2         Transform Numeric Values To Color-Gradient
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)
diffCombin              Compute Matrix Of Differences For All Pairwise
                        Combinations Of Numeric Vector
diffPPM                 Difference in ppm between numeric values
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
extrColsDeX             Flexible extraction of columns
extrNumericFromMatr     Extract numeric part of matrix or data.frame
extrSpcText             Extract Specific Text
extractLast2numericParts
                        Extract Last Two Numeric Parts From Character
                        Vector
filt3dimArr             Filter three-dimensional array of numeric data
filtSizeUniq            Filter For UniqueElements
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.
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
firstOfRepLines         Reduce To First Occurance Of Repeated Lines
firstOfRepeated         Find first of repeated elements
fuseAnnotMatr           Fuse annotation matrix to initial matrix
fuseCommonListElem      Fuse content of list-elements with redundant
                        (duplicated) names
fusePairs               Fuse pairs to generate cluster-names
get1stOfRepeatedByCol   Get First Of Repeated By Column
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.
getPairwiseSetup        Extract Pairwise Testing Setup
getValuesByUnique       Print matrix-content as plot
gitDataUrl              Convert GitHub Url-Name For Reading In Raw-Mode
htmlSpecCharConv        Html Special Character Conversion
indexGroupsFromPW       Index Names Of Groups From Vector Of
                        Concatenated Pairwise Group-Names
keepCommonText          Extract Longest Common Text Out Of Character
                        Vector
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
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
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
naOmit                  Fast na.omit
nonAmbiguousMat         Transform matrix to non-ambiguous matrix (in
                        respect to given column)
nonAmbiguousNum         Make numeric vector non-ambiguous (ie unique)
nonRedundLines          Non-Redundant Lines Of Matrix
nonredDataFrame         Filter for unique elements
normalizeThis           Normalize Data In Various Modes
numPairDeColNames       Extract pair of numeric values from vector or
                        column-names
orderMatrToRef          Order Lines of Matrix According to Reference
                        (Character) Vector
organizeAsListOfRepl    (re)organize data of (3-dim) array as list of
                        replicates
pVal2lfdr               Convert p-values to lfdr
packageDownloadStat     Simple Package Download Statistics From CRAN
pairsAsPropensMatr      Convert Pairs of Node-Names to Non-Oriented
                        Propensity Matrix
partUnlist              Partial unlist of lists of lists
partialDist             Partial distance matrix (focus on closest)
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
pwSeparatorList         Suggestions Of Collections Of Classical
                        Separators For Pairwise Combinations
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
replNAbyLow             Replace NAs By Low Balues
replPlateCV             CV of replicate plates (list of matrixes)
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
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
rowSEMs                 SEM for each row
rowSds                  sd for each row (fast execution)
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 This function draws
                        av 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
sumNAperGroup           Count number of NAs per sub-set of columns
summarizeCols           Summarize columns (as median,mean,min,last or
                        other methods)
sysDate                 System-date (compressed format)
tTestAllVal             t.test on all individual values against all
                        other values
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
trimRedundText          Trim redundant text
trimmedMean             Trimmed Mean
truncateVect            Truncating Text Vector To Specific Length
unifyEnumerator         Unify Enumerators
uniqCountReport         Report number of unique and redundant elements
                        (optional figure)
upperMaCoord            (upper) pairwise x,y combinations
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.
withinRefRange          Check For Values Within Range Of Reference
writeCsv                Write (And Convert) Csv Files
