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 | Verify File-name If Existing (in specified path), If Has... |
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 |
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... |
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... |
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... |
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-doubleExt | Return File-name Extensions Including Double Extensions (eg... |
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 (Deprecated) |
dot-trimFromStart | Trim from start (Deprecated) |
dot-trimLeft | Trim From Left Side |
dot-trimRight | Trim From Right Side |
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... |
rmOrphans | Remove or Reassign Orphan Indexes |
rmSharedWords | Trim/Remove Redundant Words |
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 | 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... |
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 |
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... |
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 |
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