| addBeforFileExtension | Add text before file-extension |
| adjBy2ptReg | Linear rescaling of numeric vertor or matrix |
| adjustUnitPrefix | Adjust Value With Different Decimal Prefixes To Single Prefix... |
| appendNR | Append vectors or lists, without duplcating common elements |
| arrayCV | CV of array |
| asSepList | Organize Data as Separate List-Entries |
| 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... |
| checkFilePath | Check If File Is Available For Reading |
| checkGrpOrder | checkGrpOrder |
| checkGrpOrderSEM | Check order of multiple groups including non-overlapping... |
| 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... |
| 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... |
| combineOverlapInfo | Find and combine points located very close in x/y space |
| combineRedBasedOnCol | Combine/reduce redundant lines based on specified column |
| combineRedundLinesInListAcRef | Combine Redundant Lines In List |
| 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... |
| conv01toColNa | Convert matrix of integer to matrix of x-times repeated... |
| 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... |
| 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... |
| countSameStartEnd | Count same start- and end- sites of edges (or fragments) |
| cutArrayInCluLike | Cut 3-dim array in list of matrixes (or arrays) similar to... |
| 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... |
| diffPPM | Difference in ppm between numeric values |
| dot-addLetterWoLast | Add letter to all elements but not last |
| dot-allRatioMatr1to2 | Calculate ratios for each column to each column of... |
| dot-allRatios | Search character-string and cut either before or after |
| dot-arrLstMean | Summarize along columns of multiple arrays in list |
| dot-arrLstSEM | Summarize along columns of mult arrays in list |
| dot-asDF2 | Convert anything to data.frame |
| dot-breakInSer | Get series of values after last discontinuity |
| dot-bringToCtr | Bring most extreme to center |
| dot-checkArgNa | Check argument names |
| dot-checkConsistentArrList | Check list of arrays for consistent dimensions of all arrays |
| dot-checkConvt2Vect | Convert to simple vector (similar to unlist) |
| dot-checkFactor | Check Factor |
| dot-checkFileNameExtensions | checkFileNameExtensions Function for checking file-names. |
| dot-checkLegendLoc | Check argument for Location of legend |
| dot-checkLmConfInt | Compare 'dat' to confindence interval of linare model 'lMod'... |
| dot-checkRegrArguments | Check regression arguments |
| dot-chooseGrpCol | Automatic choice of colors |
| dot-combineListAnnot | Combine annotation information from list of matrixes |
| dot-compareByDiff | Compare by distance/difference |
| dot-compareByLogRatio | Compare by log-ratio |
| dot-compareByPPM | Compare by PPM |
| dot-complCols | Search (complementing) columns for best coverage of non-NA... |
| dot-composeCallName | Compose sequence of (function-)calls |
| dot-convertMatrToNum | Convert numeric matrix to numeric |
| dot-convertNa | Convert/standardize names of 'query' to standard names from... |
| dot-corDuplItemsByIncrem | Avoid duplicating items between 'curNa' and 'newNa' by... |
| dot-cutAtSearch | Search character-string and cut either before or after |
| dot-cutStr | Cut string to get all variants from given start with min and... |
| dot-datSlope | Model linear regression and optional plot |
| dot-extrNAneighb | Extract NA-neighbour values |
| dot-extrNumHeadingCap | Extract number(s) before capital character |
| dot-extrNumHeadingSepChar | Extract numbers before separator followed by alphabetic... |
| dot-filterNetw | Filter nodes & edges for extracting networks (main) This... |
| dot-filterSw | Filter 3-dim array of numeric data (main) |
| dot-filtSize | Filter for size |
| dot-findBorderOverlaps | Find overlap instances among range of values in lines |
| dot-firstMin | Get first minimum |
| dot-fuse2ArrBy2ndDim | fuse 2 instances of 3dim arr as mult cols in 3dim array |
| dot-getAmean | Get A value for each group of replicates |
| dot-getAmean2 | Get A value for each group of replicates based on comp |
| dot-getMvalue2 | Get M value for each group of replicates based on comp |
| dot-growTree | Grow tree |
| dot-insp1dimByClustering | Segment (1-dim vector) 'dat' into clusters |
| dot-inspectHeader | Inspect 'matr' and check if 1st line can be used/converted as... |
| dot-keepCenter1d | Refine/filter 'dat1' (1dim dataset, eg cluster) with aim of... |
| dot-keepFiniteCol | Remove all columns where all data are not finite |
| dot-mayBeNum | Check if vector may be numeric content |
| dot-medianSpecGrp | Rescale respective to specific group |
| dot-mergeMatrices | Merge Multiple Matrices (main) |
| dot-minDif | find closest neighbour to numeric vector |
| dot-neigbDis | Distances beteenw sorted points of 2-columns |
| dot-normalize | Main Normalization function |
| dot-normConstSlope | Normalize columns of 2dim matrix to common linear regression... |
| dot-offCenter | Return position of 'di' (numeric vector) which is most... |
| dot-pasteCols | Paste-concatenate all columns of matrix |
| dot-plotCountPie | Pie plot for counting results |
| dot-plusLowerCaps | Add lower caps to character vector |
| dot-predRes | Calculate residues of (2-dim) linear model 'lMod'-prediction... |
| dot-raiseColLowest | Raise all values close to lowest value |
| dot-removeCol | Remove columns indicated by col-number |
| dot-removeEmptyCol | Search for (empty) columns conaining only entries defined in... |
| dot-replSpecChar | Replace Special Characters |
| dot-retain1stPart | Trim character string: keep only text before 'sep' |
| dot-rowGrpCV | row group CV (main) |
| dot-rowGrpMeans | row group mean (main) |
| dot-rowGrpSds | row group sd (main) |
| dot-rowGrpSums | row group rowSums per group (main) |
| dot-rowNorm | Row-normalization procedure on matrix or data.frame 'dat' |
| dot-rowNormFact | Obtain normalization factor (main) |
| dot-scale01 | Scale between 0 and 1 (main) |
| dot-scaleSpecGrp | Rescale respective to specific group |
| dot-scaleXY | Scale between min and max value (main) |
| dot-seqCutStr | Cut string to get all variants from given start with min... |
| dot-setLowestTo | Set lowest value to given value |
| dot-sortMid | Choose most frequent or middle of sorted vector |
| dot-stackArray | Reorganize array by reducing dimension 'byDim' (similar to... |
| dot-summarizeCols | Summarize columns of matrix (or data.frame) 'x' using apply... |
| dot-trimFromEnd | Trim from end |
| dot-trimFromStart | Trim from start |
| dot-trimLeft | Trim from Left |
| dot-trimRight | Trim from right |
| dot-uniqueWName | Check regression arguments |
| dot-vector2Matr | Convert numeric vector to matrix |
| 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 |
| filt3dimArr | Filter three-dimensional array of numeric data |
| filterLiColDeList | Filter lines(rows) and/or columns from all suitable elements... |
| filterList | Filter for unique elements |
| filterNetw | Filter nodes & edges for extracting networks This function... |
| 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)... |
| fusePairs | Fuse pairs to generate cluster-names |
| get1stOfRepeatedByCol | Get first of repeated by column |
| getValuesByUnique | Print matrix-content as plot |
| gitDataUrl | Convert ulr-name for reading in raw-mode |
| htmlSpecCharConv | Html special character conversion |
| keepCommonText | Extract Longest Common Text Out Of Character Vector |
| levIndex | Transform (factor) levels into index |
| linModelSelect | Test multiple starting levels for linear regression model,... |
| 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... |
| 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... |
| 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... |
| multiMatch | Simple Multi-to-Multi Matching of (Concatenated) Terms |
| naOmit | Fast na.omit |
| nFragments | Number of fragments after cut at specific character(s) within... |
| 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... |
| 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 |
| orderMatrToRef | Order Lines of Matrix According to Reference (Character)... |
| organizeAsListOfRepl | (re)organize data of (3-dim) array as list of replicates |
| 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... |
| protectSpecChar | Protect Special Characters |
| pVal2lfdr | Convert p-values to lfdr |
| randIndFx | Distance of categorical data (Jaccard, Rand and adjusted Rand... |
| 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... |
| regrMultBy1or2point | Rescaling of multiple data-sets according to reference data... |
| 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... |
| rmEnumeratorName | Remove or rename enumerator tag/name (or remove entire... |
| rnormW | Normal random number generation with close fit to expected... |
| rowCVs | rowCVs |
| rowGrpCV | Row group CV |
| rowGrpMeans | rowMeans with destinction of groups (of columns, eg groups of... |
| 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... |
| rowMedSds | sd of median for each row by bootstrap |
| rowNormalize | Row Normalize |
| rowSds | sd for each row (fast execution) |
| rowSEMs | SEM for each row |
| sampNoDeMArrayLM | Locate Sample Index From Index or Name Of Pair-Wise... |
| scaleXY | Scale data to given minimum and maxiumum |
| searchDataPairs | Search duplicated data over multiple columns, ie pairs of... |
| searchLinesAtGivenSlope | Search points forming lines at given slope |
| simpleFragFig | Simple figure showing line from start- to end-sites of edges... |
| 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) |
| 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 |
| unifyEnumerator | Unify Enumerators |
| uniqCountReport | Report number of unique and redundant elements (optional... |
| upperMaCoord | (upper) pairwise x,y combinations |
| withinRefRange | Check for values within range of reference |
| writeCsv | Write (and convert) csv files |
| XYToDiffPpm | Express difference as ppm |
