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A B C D E F G H L M N O P R S T U W X
| addBeforFileExtension | Add text before file-extension |
| adjBy2ptReg | Linear rescaling of numeric vertor or matrix |
| arrayCV | CV of array |
| asSepList | Organize data as separate list-entries |
| buildTree | Connect edges to form 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 |
| 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) value 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 |
| 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 |
| convMatr2df | Convert matrix (eg with redundant) row-names to data.frame |
| convToNum | Convert to numeric |
| correctToUnique | Correct vector to unique |
| 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 channel, of list of arrays |
| extractLast2numericParts | Extract last two numeric parts from character vector |
| extrNumericFromMatr | Extract numeric part of matrix or data.frame |
| extrSpcText | Extract specific text |
| filt3dimArr | Filter a three-dimensional array of numeric data |
| 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 |
| get1stOfRepeatedByCol | Get first of repeated by column |
| getValuesByUnique | Print matrix-content as plot |
| htmlSpecCharConv | Html special character conversion |
| 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 |
| matr2list | Transform matrix to list of vectors |
| mergeSelCol | Merge selected columns out of 2 matrix or data.frames |
| mergeSelCol3 | mergeSelCol3 |
| 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 |
| 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 |
| organizeAsListOfRepl | (re)organize data of (3-dim) array as list of replicates |
| 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 |
| pVal2lfdr | Convert p-values to lfdr |
| randIndFx | Distance of categorical dara (Jaccard,Rand and adjusted Rand index) |
| ratioAllComb | Calculate all ratios between x and y |
| ratioToPpm | Convert ratio to ppm |
| readCsvBatch | Read batch of csv-files |
| 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 |
| 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 |
| rowCVs | rowCVs |
| rowGrpCV | row group CV |
| rowGrpMeans | rowMeans with destinction of groups (of columns, eg groups of replicates) |
| 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 |
| 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) |
| stdErrMedBoot | Standard eror of median by boot-strap |
| summarizeCols | Summarize columns (as median,mean,min,last or other methods) |
| tableToPlot | Print matrix-content as plot |
| test2factLimma | 2-factorial limma-style t-test |
| treatTxtDuplicates | Locate duplicates in text and make non-redundant |
| triCoord | Pairwise x,y combinations |
| tTestAllVal | t.test on all individual values against all other values |
| uniqCountReport | Report number of unique and redundant elements (optional figure) |
| 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 |