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wrMisc (version 1.5.2)

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). Other 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. Many times large experimental datasets need some additional filtering, adequate functions are provided. Batch reading (or writing) of sets of files and combining data to arrays is supported, too. 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.

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Version

Install

install.packages('wrMisc')

Monthly Downloads

1,813

Version

1.5.2

License

GPL-3

Maintainer

Wolfgang Raffelsberger

Last Published

February 9th, 2021

Functions in wrMisc (1.5.2)

Connect edges to form tree and extract all possible branches

addBeforFileExtension

Add text before file-extension

checkGrpOrderSEM

Check order of multiple groups including non-overlapping SEM-margins

Organize data as separate list-entries

Linear rescaling of numeric vertor or matrix

cbind to non-redundant

Express difference as ppm

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

checkVectLength

Check length of vector

cleanReplicates

Replace most distant values by NA

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

contribToContigPerFrag

Characterize individual contribution of single edges in tree-structures

sd for each column

Complete list of arrays for same dimensions

Standard error of median for each column by bootstrap

Get all combinations with TRUE from each column

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

combinatIntTable

Planing for making all multiplicative combinations

colorAccording2

Transform numeric values to color-gradient

checkSimValueInSer

Check for similar values in series

Extract just one series, ie channel, of list of arrays

closeMatchMatrix

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

Filter a three-dimensional array of numeric data

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

Cut character-vector at multiple sites

extractLast2numericParts

Extract last two numeric parts from character vector

Find close numeric values between two vectors

linRegrParamAndPVal

Fit linear regression, return parameters and p-values

Find repeated elements

Compare means of two vectors by permutation test

checkStrictOrder

Check for strict (ascencing or descending) order

listBatchReplace

Replacements in list

Flexible extraction of columns

organizeAsListOfRepl

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

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

Merge Named Vectors

numPairDeColNames

Extract pair of numeric values from vector or column-names

extrNumericFromMatr

Extract numeric part of matrix or data.frame

Convert to numeric

combineByEitherFactor

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

correctToUnique

Correct vector to unique

combineOverlapInfo

Find and combine points located very close in x/y space

Extract specific text

Test multiple starting levels for linear regression model, select best and plot

htmlSpecCharConv

Html special character conversion

convColorToTransp

Assign new transparency to given colors

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

combineRedBasedOnCol

Combine/reduce redundant lines based on specified column

combineReplFromListToMatr

Combine replicates from list to matrix

Replace NAs by low values

Reorganize matrix according to clustering-output

Compute matrix of differences for all pairwise combinations of numeric vector

difference in ppm between numeric values

Filter matrix to keep only first of repeated lines

Exclude extreme values (based on distance to mean)

Normalize by adjusting exponent

firstOfRepeated

Find first of repeated elements

findSimilFrom2sets

Find similar numeric values from two vectors/matrixes

firstOfRepLines

Reduce to first occurance of repeated lines

findUsableGroupRange

Select groups within given range

Correct mixed slash and backslash in file path

countCloseToLimits

Count from two vectors number of values close within given limits

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

get1stOfRepeatedByCol

Get first of repeated by column

fuseCommonListElem

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

Merge selected columns out of 2 matrix or data.frames

nonAmbiguousNum

make numeric vector non-ambiguous (ie unique)

Fuse annotation matrix to initial matrix

matchNamesWithReverseParts

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

Make non-redundant matrix

Multiple moderated pair-wise t-tests from limma

Non-redundant lines of matrix

Fuse pairs to generate cluster-names

Number of fragments after cut at specific character(s) within size-range

getValuesByUnique

Print matrix-content as plot

Partial distance matrix (focus on closest)

Equal character-length number

Filter for unique elements

Filter for unique elements

Advanced paste-collapse

Read tabular content of files with variable number of columns

Read batch of Excel xlsx-files

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

Count number of NAs per row and group of columns

matchSampToPairw

Match names to concatenated pairs of names

Transform columns of matrix to list of vectors

Minimum distance/difference between values

nonredDataFrame

Filter for unique elements

Normalize data in various modes

Moderated pair-wise t-test from limma

regrMultBy1or2point

Rescaling of multiple data-sets according to reference data using regression

singleLineAnova

2-factorial Anova on single line of data

listGroupsByNames

Organize values into list and sort by names

Convert ratio to ppm

make MA-List object

Run lm on segmented data (from clustering)

nonAmbiguousMat

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

sortBy2CategorAnd1IntCol

Sort matrix by two categorical and one integer columns

Number of fragments after cut at specific character(s)

Count number of non-numeric characters

searchLinesAtGivenSlope

Search points forming lines at given slope

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)

Print matrix-content as plot

Convert p-values to lfdr

Read batch of csv-files

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

Filter lines of matrix for max number of NAs

rankToContigTab

Contingenty tables for fit of ranking

Calculate all ratios between x and y

CV of replicate plates (list of matrixes)

Pairwise x,y combinations

Partial unlist of lists of lists

Reduce table by aggregating smaller groups

2-factorial limma-style t-test

Estimate mode (most frequent value)

uniqCountReport

Report number of unique and redundant elements (optional figure)

Remove lines of matrix redundant /duplicated for 1st and 2nd column

(upper) pairwise x,y combinations

regrBy1or2point

Rescaling according to reference data using linear regression.

Per line and per group sd-values

Scale data to given minimum and maxiumum

Standardize (scale) data

SEM for each row

sd of median for each row by bootstrap

searchDataPairs

Search duplicated data over multiple columns, ie pairs of data

Check for values within range of reference

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

treatTxtDuplicates

Locate duplicates in text and make non-redundant

Make single vector gray-gradient

sd for each row (fast execution)

Count number of NAs per sub-set of columns

Standard eror of median by boot-strap

Write (and convert) csv files

t.test on all individual values against all other values