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wrMisc (version 2.1.0)

Analyze Experimental High-Throughput (Omics) Data

Description

The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions. Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc. Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM) for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates). A group of functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc. Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values. Other functions help aligning a matrix or data.frame to a reference using partial matching or to mine an experimental setup to extract patterns of replicate samples. Many times large experimental datasets need some additional filtering, adequate functions are provided. Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too. Batch reading (or writing) of sets of files and combining data to arrays is supported, too.

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Version

Install

install.packages('wrMisc')

Monthly Downloads

1,568

Version

2.1.0

License

GPL-3

Maintainer

Wolfgang Raffelsberger

Last Published

June 8th, 2026

Functions in wrMisc (2.1.0)

Organize Data as Separate List-Entries

addBeforFileExtension

Add Text Before File-Extension

Connect edges to from tree and extract all possible branches

Append vectors or lists, without duplcating common elements

Express difference as ppm

addBeforeFileExtension

Add Text Before File-Extension

Normalize Blockwise Two Or Three Datasets

adjustUnitPrefix

Adjust Value With Different Decimal Prefixes To Single Prefix Plus Unit

Adjust Values By Two-Point Regression

checkVectLength

Check length of vector

checkUnitPrefix

Check For Common Unit-Name in Text

Check how multiple groups of data separate or overlap based on mean +/- sd

checkStrictOrder

Check for strict (ascencing or descending) order

checkSimValueInSer

Check for similar values in series

Verify File-name If Existing (in specified path), If Has Proper Extension Or Select Files With Proper Extension From Given Path

checkGrpOrderSEM

Check Order Of Multiple Groups Including Non-Overlapping SEM-Margins

cbind to non-redundant

chooseGroupNames

Choose Column Most Likely For Sample-Names

closeMatchMatrix

Reorganize results of search for close (similar) values in matrix-view

combineByEitherFactor

Create factor-like column regrouping data regrouping simultaneaously by two factors

sd for each column

colorAccording2

Transform Numeric Values To Color-Gradient

Combine Vectors From List And Return Basic Count Statistics

combinatIntTable

Planing for making all multiplicative combinations

Standard Error Of Median For Each Column By Bootstrap

cleanReplicates

Replace Most Distant Values by NA

Compare Means Of Two Vectors By Permutation Test

Confidence Interval To Given Alpha

combineReplFromListToMatr

Combine replicates from list to matrix

contribToContigPerFrag

Characterize individual contribution of single edges in tree-structures

combineRedBasedOnCol

Combine/reduce redundant lines based on specified column

Get All Combinations With TRUE From Each Column

combineRedundLinesInList

Combine Redundant Lines In List

combineRedundLinesInListAcRef

Combine Redundant Lines In List, Deprecated

Complete list of arrays for same dimensions

Value Matching With Option For Concatenated Terms

combineOverlapInfo

Find And Combine Points Located Very Close In x/y Space

Convert matrix (eg with redundant) row-names to data.frame

countCloseToLimits

Count From Two Vectors Number Of Values Close Within Given Limits

countSameStartEnd

Count Same Start- And End- Sites Of Edges (Or Fragments)

Convert matrix of integer to matrix of x-times repeated column-names

convColorToTransp

Assign new transparency to given colors

convPairwiseSetup

Check Comparison-Choice

correctToUnique

Correct vector to unique

get coordinates of values/points in matrix according to filtering condition

Convert Vector To Numeric

Correct Mixed Slash And Backslash In File-Path

Difference in ppm between numeric values

.allRatioMatr1to2

Calculate ratios for each column to each column of reference-matrix

Cut numeric vector to n groups (ie convert to factor)

Summarize along columns of multiple arrays in list

Compute Matrix Of Differences For All Pairwise Combinations Of Numeric Vector

.addLetterWoLast

Add letter to all elements but not last

Search character-string and cut either before or after

cutArrayInCluLike

Cut 3-dim array in list of matrixes (or arrays) similar to organizing into clusters

Cut character-vector at multiple sites

Summarize along columns of mult arrays in list

Get series of values after last discontinuity

Bring most extreme to center

Check argument names

Convert anything to data.frame

.checkFileNameExtensions

Check File Name Extensions Function for checking file-names.

.checkConsistentArrList

Check list of arrays for consistent dimensions of all arrays

.checkLegendLoc

Check argument for Location of legend

.checkLmConfInt

Compare 'dat' to confindence interval of linare model 'lMod' (eg from lm())

.checkConvt2Vect

Convert To Simple Vector (similar to unlist)

Compare by distance/difference

.convertMatrToNum

Convert numeric matrix to numeric

.checkRegrArguments

Check regression arguments

.combineListAnnot

Combine annotation information from list of matrixes

Automatic choice of colors

Search (complementing) Columns For Best Coverage Of Non-NA Data For rowNormalization (main)

Convert/standardize names of 'query' to standard names from 'ref'

.compareByLogRatio

Compare by log-ratio

.composeCallName

Compose Sequence Of (Function-)Calls

Search character-string and cut either before or after

.corDuplItemsByIncrem

Avoid duplicating items between 'curNa' and 'newNa' by incrementing digits after 'extPref' (in newNa)

.extrNumHeadingCap

Extract number(s) before capital character

Extract NA-neighbour values

.extrNumHeadingSepChar

Extract numbers before separator followed by alphabetic character

Filter for size

Model linear regression and optional plot

Cut string to get all variants from given start with min and max length

Return File-name Extensions Including Double Extensions (eg txt.gz)

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.

Filter 3-dim array of numeric data (main)

.getPWseparator

Find Separator In Vector Of Pairwise Group-Names This function allows identifing separator used when pairwise groups are presented.

Get first minimum

.findBorderOverlaps

Find overlap instances among range of values in lines

.fuse2ArrBy2ndDim

fuse 2 instances of 3dim arr as mult cols in 3dim array

Get A value for each group of replicates based on comp

Get M value for each group of replicates based on comp

Get A value for each group of replicates

.insp1dimByClustering

Segment (1-dim vector) 'dat' into clusters

Refine/filter 'dat1' (1dim dataset, eg cluster) with aim of keeping center of data

Distances beteenw sorted points of 2-columns

Check if vector may be numeric content

Remove all columns where all data are not finite

find closest neighbour to numeric vector

Rescale respective to specific group

Merge Multiple Matrices (main)

Inspect 'matr' and check if 1st line can be used/converted as header

Main Normalization function

.normConstSlope

Normalize Columns Of 2-dim Matrix To Common Linear Regression Fit

.removeEmptyCol

Search for (empty) columns conaining only entries defined in 'searchFields' and remove such columns

Pie plot for counting results

Remove columns indicated by col-number

Add lower caps to character vector

Calculate residues of (2-dim) linear model 'lMod'-prediction of/for 'dat'

row group CV (main)

.raiseColLowest

Raise all values close to lowest value

Replace Special Characters

Paste-concatenate all columns of matrix

Trim character string: keep only text before 'sep'

Scale between 0 and 1 (main)

Row-normalization Procedure On Matrix Or Data.frame (main)

row group mean (main)

row group rowSums per group (main)

Rescale respective to specific group

Cut string to get all variants from given start with min length, depreciated

Scale between min and max value (main)

Obtain Normalization Factor (main)

row group sd (main)

Set lowest value to given value

Check regression arguments

Trim From Right Side

Reorganize array by reducing dimension 'byDim' (similar to stack() for data-frames)

Convert numeric vector to matrix

Trim From Left Side

Choose most frequent or middle of sorted vector

Trim from start (Deprecated)

Eliminate close (overlapping) points (in x & y space)

Summarize columns of matrix (or data.frame) 'x' using apply (main)

Trim from end (Deprecated)

Filter For UniqueElements

Filter three-dimensional array of numeric data

extrNumericFromMatr

Extract numeric part of matrix or data.frame

Exclude Extreme Values (Based On Distance To Mean)

Equal character-length number

extractLast2numericParts

Extract Last Two Numeric Parts From Character Vector

Extract Just One Series, ie One Channel, Of List Of Arrays

Normalize By Adjusting Exponent

Flexible extraction of columns

Extract Specific Text

Filter matrix to keep only first of repeated lines

firstOfRepLines

Reduce To First Occurance Of Repeated Lines

Find Close Numeric Values Between Two Vectors

findSimilFrom2sets

Find similar numeric values from two vectors/matrixes

findHeadAndTail

Find Group-Names In Pairwise Combined And Isolate Separator

filterLiColDeList

Filter lines(rows) and/or columns from all suitable elements of list

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.

Filter for unique elements

findUsableGroupRange

Select Groups Within Given Range

Find repeated elements

fuseCommonListElem

Fuse content of list-elements with redundant (duplicated) names

Identify Separator In Pairwise Group-Names Or Find Separator For Use With Pairwise Group-Names This function allows identifing separator used when pairwise groups are presented.

Convert GitHub Url-Name For Reading In Raw-Mode

firstOfRepeated

Find first of repeated elements

get1stOfRepeatedByCol

Get First Of Repeated By Column

htmlSpecCharConv

Html Special Character Conversion

getValuesByUnique

Print matrix-content as plot

getPairwiseSetup

Extract Pairwise Testing Setup

Fuse annotation matrix to initial matrix

Fuse pairs to generate cluster-names

Extract Longest Common Text Out Of Character Vector

Run lm on segmented data (from clustering)

Make MA-List Object

indexGroupsFromPW

Index Names Of Groups From Vector Of Concatenated Pairwise Group-Names

listGroupsByNames

Organize Values Into List And Sort By Names

listBatchReplace

Replacements in list

Transform (factor) levels into index

linRegrParamAndPVal

Fit linear regression, return parameters and p-values

Test Multiple Starting Levels For Linear Regression Model, Select Best And Plot

Merge selected columns out of 2 matrix or data.frames

mergeMatrixList

Merge Multiple Matrices from List

Transform columns of matrix to list of vectors

matchSampToPairw

Match Names To Concatenated Pairs Of Names

Make non-redundant matrix

matchNamesWithReverseParts

Value Matching with optional reversing of sub-parts of non-matching elements

matchMatrixLinesToRef

Match All Lines of Matrix To Reference Note

Merge Named Vectors

Merge Multiple Matrices

Count number of non-numeric characters

Simple Multi-to-Multi Matching of (Concatenated) Terms

Multiple Moderated Pairwise t-tests From limma

Number Of Fragments After Cut At Specific Character(s) Within Size-range

Minimum distance/difference between values

Extended version of merge for multiple objects (even without rownames)

Number Of Fragments After Cut At Specific Character(s)

Moderated Pairwise t-test From Limma

multiCharReplace

Multiple replacement of entire character elements in simple vector, matrix or data.frame

packageDownloadStat

Simple Package Download Statistics From CRAN

nonAmbiguousMat

Transform matrix to non-ambiguous matrix (in respect to given column)

Order Lines of Matrix According to Reference (Character) Vector

Non-Redundant Lines Of Matrix

Normalize Data In Various Modes

nonAmbiguousNum

Make numeric vector non-ambiguous (ie unique)

nonredDataFrame

Filter for unique elements

Convert p-values to lfdr

organizeAsListOfRepl

(re)organize data of (3-dim) array as list of replicates

numPairDeColNames

Extract pair of numeric values from vector or column-names

presenceGrpFilt

Filter For Each Group Of Columns For Sufficient Data As Non-NA

Advanced paste-collapse

pwSeparatorList

Suggestions Of Collections Of Classical Separators For Pairwise Combinations

Partial distance matrix (focus on closest)

Distance of categorical data (Jaccard, Rand and adjusted Rand index)

Partial unlist of lists of lists

pairsAsPropensMatr

Convert Pairs of Node-Names to Non-Oriented Propensity Matrix

protectSpecChar

Protect Special Characters

rankToContigTab

Contingenty tables for fit of ranking

Filter Lines Of Matrix For Max Number Of NAs

Calculate all ratios between x and y

Read Batch of Excel xlsx-Files

Convert ratio to ppm

regrBy1or2point

Rescaling According To Reference Data Using Linear Regression.

Reduce table by aggregating smaller groups

readTabulatedBatch

Batch Reading Of Tabulated Text-Files

Read Tabular Content Of Files With Variable Number Of Columns

Read batch of csv-files

regrMultBy1or2point

Rescaling Of Multiple Data-Sets According To Reference Data Using Regression

rmEnumeratorName

Remove or rename enumerator tag/name (or remove entire enumerator) from tailing enumerators

Remove or Reassign Orphan Indexes

Reorganize matrix according to clustering-output

Trim/Remove Redundant Words

CV of replicate plates (list of matrixes)

replacePWseparator

Replace Separator In Vector Of Pairwise Group-Names This function allows identifying and substituting a separator used in a character vector concatenated of pairwise groups.

Remove Lines Of Matrix Redundant /Duplicated For 1st And 2nd Column

replicateStructure

Search and Select Groups of Replicates

Normal random number generation with close fit to expected mean and sd

Replace NAs by low values

Estimate sd Of Median For Each Row By Bootstrap

rowSums with destinction of groups (of columns, eg groups of replicates)

Row-Means With Destinction Of Groups (Of Columns, eg Groups Of Replicates)

Per line and per group sd-values

sd for each row (fast execution)

Count Number Of NAs Per Row And Group Of Columns

SEM for each row

sortBy2CategorAnd1IntCol

Sort matrix by two categorical and one integer columns

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)

searchLinesAtGivenSlope

Search Points Forming Lines At Given Slope

sampNoDeMArrayLM

Locate Sample Index From Index Or Name Of Pair-Wise Comparisons In List Or MArrayLM-Object

searchDataPairs

Search duplicated data over multiple columns, ie pairs of data

singleLineAnova

2-factorial Anova on single line of data

Rescale Data To Given Minimum- And Maxiumum- Values

Estimate Mode (Most Frequent Value)

sortByNRepeated

Make a list of common occurances sorted by number of repeats

Standardize (scale) data

Make single vector gray-gradient

Print matrix-content as plot

Summarize columns (as median,mean,min,last or other methods)

t.test on all individual values against all other values

Mean Of 3 Highest Values

treatTxtDuplicates

Locate duplicates in text and make non-redundant

System-date (compressed format)

Count number of NAs per sub-set of columns

Standard Eror Of Median by Boot-Strap

2-Factorial Limma-Style t-Test

unifyEnumerator

Unify Enumerators

vectorDistAngle

Vector Distance and Angle

Check For Values Within Range Of Reference

Write (And Convert) Csv Files

Trim redundant text

Pairwise x,y Combinations

uniqCountReport

Report number of unique and redundant elements (optional figure)

(upper) pairwise x,y combinations

Filter Statistical Testing Results in Volcano-Plot Like Fashion This function allows filtering statistical testing results combined with M-values (log2 fold-change) and other filtering criteria. All suitable values can be extracted from objects created from package wrProteo (and limma) may get used automatically. The outcome can be used for Volcano-plots or exporting tables.