A B C D E F G H K L M N O P R S T U W X misc
| addBeforFileExtension | Add text before file-extension |
| adjBy2ptReg | Linear rescaling of numeric vertor or matrix |
| 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 |
| 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 | 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 |
| checkUnitPrefix | Check For Common Unit-Name in Text |
| 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 |
| colCVs | rowCVs |
| 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 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 |
| 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 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 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 |
| 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, 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 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 |
| 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 |
| orderMatrToRef | Order Lines of Matrix According to Reference (Character) Vector |
| 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 non-NA |
| protectSpecChar | Protect Special Characters |
| pVal2lfdr | Convert p-values to lfdr |
| 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 |
| 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 |
| 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 | 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 |
| 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 |
| rowSds | sd for each row (fast execution) |
| rowSEMs | SEM for each row |
| 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 |
| 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 |
| 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 |
| trimmedMean | Trimmed Mean |
| 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 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 |
| .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 | checkFileNameExtensions 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 |
| .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) |
| .filtSize | Filter for size |
| .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 |
| .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 |
| .normalize | Main Normalization function |
| .normConstSlope | Normalize columns of 2dim matrix to common linear regression fit |
| .offCenter | Return position of 'di' (numeric vector) which is most excentric (distant to 0), starts with NAs as most excentric |
| .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 'dat' |
| .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 |