| Add letter to all elements but not last | .addLetterWoLast |
| Calculate ratios for each column to each column of reference-matrix | .allRatioMatr1to2 |
| Search character-string and cut either before or after | .allRatios |
| Summarize along columns of multiple arrays in list | .arrLstMean |
| Summarize along columns of mult arrays in list | .arrLstSEM |
| Convert anything to data.frame | .asDF2 |
| Get series of values after last discontinuity | .breakInSer |
| Bring most extreme to center | .bringToCtr |
| Check argument names | .checkArgNa |
| Check list of arrays for consistent dimensions of all arrays | .checkConsistentArrList |
| Convert to simple vector (similar to unlist) | .checkConvt2Vect |
| Check Factor | .checkFactor |
| checkFileNameExtensions Function for checking file-names. | .checkFileNameExtensions |
| Check argument for Location of legend | .checkLegendLoc |
| Compare 'dat' to confindence interval of linare model 'lMod' (eg from lm()) | .checkLmConfInt |
| Check regression arguments | .checkRegrArguments |
| Automatic choice of colors | .chooseGrpCol |
| Combine annotation information from list of matrixes | .combineListAnnot |
| Compare by distance/difference | .compareByDiff |
| Compare by log-ratio | .compareByLogRatio |
| Compare by PPM | .compareByPPM |
| Search (complementing) columns for best coverage of non-NA data for rowNormalization (main) | .complCols |
| Compose sequence of (function-)calls | .composeCallName |
| Convert numeric matrix to numeric | .convertMatrToNum |
| Convert/standardize names of 'query' to standard names from 'ref' | .convertNa |
| Avoid duplicating items between 'curNa' and 'newNa' by incrementing digits after 'extPref' (in newNa) | .corDuplItemsByIncrem |
| Search character-string and cut either before or after | .cutAtSearch |
| Cut string to get all variants from given start with min and max length | .cutStr |
| Model linear regression and optional plot | .datSlope |
| Extract NA-neighbour values | .extrNAneighb |
| Extract number(s) before capital character | .extrNumHeadingCap |
| Extract numbers before separator followed by alphabetic character | .extrNumHeadingSepChar |
| 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. | .filterNetw |
| Filter 3-dim array of numeric data (main) | .filterSw |
| Filter for size | .filtSize |
| Find overlap instances among range of values in lines | .findBorderOverlaps |
| Get first minimum | .firstMin |
| fuse 2 instances of 3dim arr as mult cols in 3dim array | .fuse2ArrBy2ndDim |
| Get A value for each group of replicates | .getAmean |
| Get A value for each group of replicates based on comp | .getAmean2 |
| Get M value for each group of replicates based on comp | .getMvalue2 |
| Grow tree | .growTree |
| Segment (1-dim vector) 'dat' into clusters | .insp1dimByClustering |
| Inspect 'matr' and check if 1st line can be used/converted as header | .inspectHeader |
| Refine/filter 'dat1' (1dim dataset, eg cluster) with aim of keeping center of data | .keepCenter1d |
| Remove all columns where all data are not finite | .keepFiniteCol |
| Check if vector may be numeric content | .mayBeNum |
| Rescale respective to specific group | .medianSpecGrp |
| Merge Multiple Matrices (main) | .mergeMatrices |
| find closest neighbour to numeric vector | .minDif |
| Distances beteenw sorted points of 2-columns | .neigbDis |
| Main Normalization function | .normalize |
| Normalize columns of 2dim matrix to common linear regression fit | .normConstSlope |
| Return position of 'di' (numeric vector) which is most excentric (distant to 0), starts with NAs as most excentric | .offCenter |
| Paste-concatenate all columns of matrix | .pasteCols |
| Pie plot for counting results | .plotCountPie |
| Add lower caps to character vector | .plusLowerCaps |
| Calculate residues of (2-dim) linear model 'lMod'-prediction of/for 'dat' | .predRes |
| Raise all values close to lowest value | .raiseColLowest |
| Remove columns indicated by col-number | .removeCol |
| Search for (empty) columns conaining only entries defined in 'searchFields' and remove such columns | .removeEmptyCol |
| Replace Special Characters | .replSpecChar |
| Trim character string: keep only text before 'sep' | .retain1stPart |
| row group CV (main) | .rowGrpCV |
| row group mean (main) | .rowGrpMeans |
| row group sd (main) | .rowGrpSds |
| row group rowSums per group (main) | .rowGrpSums |
| Row-normalization procedure on matrix or data.frame 'dat' | .rowNorm |
| Obtain normalization factor (main) | .rowNormFact |
| Scale between 0 and 1 (main) | .scale01 |
| Rescale respective to specific group | .scaleSpecGrp |
| Scale between min and max value (main) | .scaleXY |
| Cut string to get all variants from given start with min length, depreciated | .seqCutStr |
| Set lowest value to given value | .setLowestTo |
| Choose most frequent or middle of sorted vector | .sortMid |
| Reorganize array by reducing dimension 'byDim' (similar to stack() for data-frames) | .stackArray |
| Summarize columns of matrix (or data.frame) 'x' using apply (main) | .summarizeCols |
| Trim from end (Deprecated) | .trimFromEnd |
| Trim from start (Deprecated) | .trimFromStart |
| Trim From Left Side | .trimLeft |
| Trim From Right Side | .trimRight |
| Check regression arguments | .uniqueWName |
| Convert numeric vector to matrix | .vector2Matr |
| Add text before file-extension | addBeforFileExtension |
| Linear rescaling of numeric vertor or matrix | adjBy2ptReg |
| Adjust Value With Different Decimal Prefixes To Single Prefix Plus Unit | adjustUnitPrefix |
| Append vectors or lists, without duplcating common elements | appendNR |
| CV of array | arrayCV |
| Organize Data as Separate List-Entries | asSepList |
| Connect edges to from tree and extract all possible branches | buildTree |
| cbind to non-redundant | cbindNR |
| Check how multiple groups of data separate or overlap based on mean +/- sd | checkAvSd |
| Check If File Is Available For Reading | checkFilePath |
| checkGrpOrder | checkGrpOrder |
| Check order of multiple groups including non-overlapping SEM-margins | checkGrpOrderSEM |
| Check for similar values in series | checkSimValueInSer |
| Check for strict (ascencing or descending) order | checkStrictOrder |
| Check For Common Unit-Name in Text | checkUnitPrefix |
| Check length of vector | checkVectLength |
| Replace Most Distant Values by NA | cleanReplicates |
| Reorganize results of search for close (similar) values in matrix-view | closeMatchMatrix |
| Compare Means Of Two Vectors By Permutation Test | coinPermTest |
| rowCVs | colCVs |
| Standard Error Of Median For Each Column By Bootstrap | colMedSds |
| Transform Numeric Values To Color-Gradient | colorAccording2 |
| sd for each column | colSds |
| Planing for making all multiplicative combinations | combinatIntTable |
| Combine Vectors From List And Return Basic Count Statistics | combineAsN |
| Create factor-like column regrouping data regrouping simultaneaously by two factors | combineByEitherFactor |
| Find and combine points located very close in x/y space | combineOverlapInfo |
| Combine/reduce redundant lines based on specified column | combineRedBasedOnCol |
| Combine Redundant Lines In List | combineRedundLinesInList |
| Combine Redundant Lines In List, Deprecated | combineRedundLinesInListAcRef |
| Combine replicates from list to matrix | combineReplFromListToMatr |
| Get all combinations with TRUE from each column | combineSingleT |
| Complete list of arrays for same dimensions | completeArrLst |
| Value Matching With Option For Concatenated Terms | concatMatch |
| Confidence Interval To Given Alpha | confInt |
| Characterize individual contribution of single edges in tree-structures | contribToContigPerFrag |
| Convert matrix of integer to matrix of x-times repeated column-names | conv01toColNa |
| Assign new transparency to given colors | convColorToTransp |
| Convert matrix (eg with redundant) row-names to data.frame | convMatr2df |
| Convert Vector To Numeric | convToNum |
| get coordinates of values/points in matrix according to filtering condition | coordOfFilt |
| Correct vector to unique | correctToUnique |
| Correct mixed slash and backslash in file path | correctWinPath |
| Count from two vectors number of values close within given limits | countCloseToLimits |
| Count same start- and end- sites of edges (or fragments) | countSameStartEnd |
| Cut 3-dim array in list of matrixes (or arrays) similar to organizing into clusters | cutArrayInCluLike |
| Cut character-vector at multiple sites | cutAtMultSites |
| Cut numeric vector to n groups (ie convert to factor) | cutToNgrp |
| Compute matrix of differences for all pairwise combinations of numeric vector | diffCombin |
| Difference in ppm between numeric values | diffPPM |
| Eliminate close (overlapping) points (in x & y space) | elimCloseCoord |
| Equal character-length number | equLenNumber |
| Exclude extreme values (based on distance to mean) | exclExtrValues |
| Normalize by adjusting exponent | exponNormalize |
| Extract just one series, ie channel, of list of arrays | extr1chan |
| Extract last two numeric parts from character vector | extractLast2numericParts |
| Flexible extraction of columns | extrColsDeX |
| Extract numeric part of matrix or data.frame | extrNumericFromMatr |
| Extract specific text | extrSpcText |
| Filter three-dimensional array of numeric data | filt3dimArr |
| Filter lines(rows) and/or columns from all suitable elements of list | filterLiColDeList |
| Filter for unique elements | filterList |
| 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. | filterNetw |
| Filter for unique elements | filtSizeUniq |
| Find close numeric values between two vectors | findCloseMatch |
| Find repeated elements | findRepeated |
| Find similar numeric values from two vectors/matrixes | findSimilFrom2sets |
| Select groups within given range | findUsableGroupRange |
| Filter matrix to keep only first of repeated lines | firstLineOfDat |
| Find first of repeated elements | firstOfRepeated |
| Reduce to first occurance of repeated lines | firstOfRepLines |
| Fuse annotation matrix to initial matrix | fuseAnnotMatr |
| Fuse content of list-elements with redundant (duplicated) names | fuseCommonListElem |
| Fuse pairs to generate cluster-names | fusePairs |
| Get first of repeated by column | get1stOfRepeatedByCol |
| Print matrix-content as plot | getValuesByUnique |
| Convert ulr-name for reading in raw-mode | gitDataUrl |
| Html Special Character Conversion | htmlSpecCharConv |
| Extract Longest Common Text Out Of Character Vector | keepCommonText |
| Transform (factor) levels into index | levIndex |
| Test multiple starting levels for linear regression model, select best and plot | linModelSelect |
| Fit linear regression, return parameters and p-values | linRegrParamAndPVal |
| Replacements in list | listBatchReplace |
| Organize values into list and sort by names | listGroupsByNames |
| Run lm on segmented data (from clustering) | lmSelClu |
| rbind on lists | lrbind |
| Make MA-List Object | makeMAList |
| Make non-redundant matrix | makeNRedMatr |
| Match All Lines of Matrix To Reference Note | matchMatrixLinesToRef |
| Value Matching with optional reversing of sub-parts of non-matching elements | matchNamesWithReverseParts |
| Match names to concatenated pairs of names | matchSampToPairw |
| Transform columns of matrix to list of vectors | matr2list |
| Merge Multiple Matrices | mergeMatrices |
| Merge Multiple Matrices from List | mergeMatrixList |
| Merge selected columns out of 2 matrix or data.frames | mergeSelCol |
| mergeSelCol3 | mergeSelCol3 |
| Merge Named Vectors | mergeVectors |
| Extended version of merge for multiple objects (even without rownames) | mergeW2 |
| Minimum distance/difference between values | minDiff |
| Moderated Pair-Wise t-test From Limma | moderTest2grp |
| Multiple moderated pair-wise t-tests from limma | moderTestXgrp |
| Multiple replacement of entire character elements in simple vector, matrix or data.frame | multiCharReplace |
| Simple Multi-to-Multi Matching of (Concatenated) Terms | multiMatch |
| Fast na.omit | naOmit |
| Number of fragments after cut at specific character(s) within size-range | nFragments |
| Number of fragments after cut at specific character(s) | nFragments0 |
| Count number of non-numeric characters | nNonNumChar |
| Transform matrix to non-ambiguous matrix (in respect to given column) | nonAmbiguousMat |
| make numeric vector non-ambiguous (ie unique) | nonAmbiguousNum |
| Filter for unique elements | nonredDataFrame |
| Non-redundant lines of matrix | nonRedundLines |
| Normalize Data In Various Modes | normalizeThis |
| Extract pair of numeric values from vector or column-names | numPairDeColNames |
| Order Lines of Matrix According to Reference (Character) Vector | orderMatrToRef |
| (re)organize data of (3-dim) array as list of replicates | organizeAsListOfRepl |
| Simple Package Download Statistics From CRAN | packageDownloadStat |
| Convert Pairs of Node-Names to Non-Oriented Propensity Matrix | pairsAsPropensMatr |
| Partial distance matrix (focus on closest) | partialDist |
| Partial unlist of lists of lists | partUnlist |
| Advanced paste-collapse | pasteC |
| Filter lines of matrix for max number of NAs | presenceFilt |
| Filter for each group of columns for sufficient data as non-NA | presenceGrpFilt |
| Protect Special Characters | protectSpecChar |
| Convert p-values to lfdr | pVal2lfdr |
| Distance of categorical data (Jaccard, Rand and adjusted Rand index) | randIndFx |
| Contingenty tables for fit of ranking | rankToContigTab |
| Calculate all ratios between x and y | ratioAllComb |
| Convert ratio to ppm | ratioToPpm |
| Read batch of csv-files | readCsvBatch |
| Batch Reading Of Tabulated Text-Files | readTabulatedBatch |
| Read Tabular Content Of Files With Variable Number Of Columns | readVarColumns |
| Read Batch of Excel xlsx-Files | readXlsxBatch |
| Reduce table by aggregating smaller groups | reduceTable |
| Rescaling according to reference data using linear regression. | regrBy1or2point |
| Rescaling of multiple data-sets according to reference data using regression | regrMultBy1or2point |
| Rename columns | renameColumns |
| Reorganize matrix according to clustering-output | reorgByCluNo |
| Search and Select Groups of Replicates | replicateStructure |
| Replace NAs by low values | replNAbyLow |
| CV of replicate plates (list of matrixes) | replPlateCV |
| Remove lines of matrix redundant /duplicated for 1st and 2nd column | rmDupl2colMatr |
| Remove or rename enumerator tag/name (or remove entire enumerator) from tailing enumerators | rmEnumeratorName |
| Remove or Reassign Orphan Indexes | rmOrphans |
| Trim/Remove Redundant Words | rmSharedWords |
| Normal random number generation with close fit to expected mean and sd | rnormW |
| rowCVs | rowCVs |
| Row group CV | rowGrpCV |
| rowMeans with destinction of groups (of columns, eg groups of replicates) | rowGrpMeans |
| Count number of NAs per row and group of columns | rowGrpNA |
| Per line and per group sd-values | rowGrpSds |
| rowSums with destinction of groups (of columns, eg groups of replicates) | rowGrpSums |
| Estimate sd Of Median For Each Row By Bootstrap | rowMedSds |
| Row Normalize | rowNormalize |
| sd for each row (fast execution) | rowSds |
| SEM for each row | rowSEMs |
| Locate Sample Index From Index Or Name Of Pair-Wise Comparisons In List Or MArrayLM-Object | sampNoDeMArrayLM |
| Scale data to given minimum and maxiumum | scaleXY |
| Search duplicated data over multiple columns, ie pairs of data | searchDataPairs |
| Search Points Forming Lines At Given Slope | searchLinesAtGivenSlope |
| 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) | simpleFragFig |
| 2-factorial Anova on single line of data | singleLineAnova |
| Sort matrix by two categorical and one integer columns | sortBy2CategorAnd1IntCol |
| Make a list of common occurances sorted by number of repeats | sortByNRepeated |
| Estimate Mode (Most Frequent Value) | stableMode |
| Standardize (scale) data | standardW |
| Standard Eror Of Median by Boot-Strap | stdErrMedBoot |
| Summarize columns (as median,mean,min,last or other methods) | summarizeCols |
| Count number of NAs per sub-set of columns | sumNAperGroup |
| System-date (compressed format) | sysDate |
| Print matrix-content as plot | tableToPlot |
| 2-Factorial Limma-Style t-Test | test2factLimma |
| Make single vector gray-gradient | transpGraySca |
| Locate duplicates in text and make non-redundant | treatTxtDuplicates |
| Pairwise x,y combinations | triCoord |
| Trimmed Mean | trimmedMean |
| Trim redundant text | trimRedundText |
| t.test on all individual values against all other values | tTestAllVal |
| Unify Enumerators | unifyEnumerator |
| Report number of unique and redundant elements (optional figure) | uniqCountReport |
| (upper) pairwise x,y combinations | upperMaCoord |
| Check for values within range of reference | withinRefRange |
| Write (and convert) csv files | writeCsv |
| Express difference as ppm | XYToDiffPpm |
