Analyze Experimental High-Throughput (Omics) Data

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... |

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 |

combineReplFromListToMatr | Combine replicates from list to matrix |

combineSingleT | Get all combinations with TRUE from each column |

completeArrLst | Complete list of arrays for same dimensions |

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 |

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