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 |
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 |
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) 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 |
combinatIntTable | Planing for making all multiplicative combinations |
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 |
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 a 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 |
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 |
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 |
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 |
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 Numerous network query tools produce a listing of pairs of nodes (with one pair of nodes per line). Using this function such a matrix (or data.frame) can be combined to this more comprehensive view as propensity-matrix. Note, this has been primarily developed for undireted interaction networks, the resulting propensity-matrix does not show any orientation any more. In a number of applications (eg in protein-protein interaction networks, PPI) the resulting matrix may be rather sparse. |
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 |
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 This function allows batch reading of multiple tabulated text files. The files can be designed specifically, alternatively all files from a given directory can be read. If package data.table is available, fast reading of files will be performed using the function 'fread'. |
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 |
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 |
rowMedSds | sd of median for each row by bootstrap |
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 |
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 |
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 |