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wrMisc (version 1.7.0)

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). 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

1,415

Version

1.7.0

License

GPL-3

Maintainer

Wolfgang Raffelsberger

Last Published

October 28th, 2021

Functions in wrMisc (1.7.0)

Linear rescaling of numeric vertor or matrix

Express difference as ppm

checkVectLength

Check length of vector

addBeforFileExtension

Add text before file-extension

combinatIntTable

Planing for making all multiplicative combinations

colorAccording2

Transform numeric values to color-gradient

countSameStartEnd

Count same start- and end- sites of edges (or fragments)

countCloseToLimits

Count from two vectors number of values close within given limits

Filter a three-dimensional array of numeric data

Flexible extraction of columns

extrNumericFromMatr

Extract numeric part of matrix or data.frame

Filter for unique elements

Fuse pairs to generate cluster-names

get1stOfRepeatedByCol

Get first of repeated by column

cleanReplicates

Replace most distant values by NA

checkGrpOrderSEM

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

checkSimValueInSer

Check for similar values in series

matchNamesWithReverseParts

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

matchSampToPairw

Match names to concatenated pairs of names

combineRedBasedOnCol

Combine/reduce redundant lines based on specified column

Compare means of two vectors by permutation test

closeMatchMatrix

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

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

checkStrictOrder

Check for strict (ascencing or descending) order

contribToContigPerFrag

Characterize individual contribution of single edges in tree-structures

combineByEitherFactor

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

combineReplFromListToMatr

Combine replicates from list to matrix

Convert vector to numeric

combineOverlapInfo

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

Normalize by adjusting exponent

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

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

Extract specific text

organizeAsListOfRepl

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

correctToUnique

Correct vector to unique

cbind to non-redundant

Find repeated elements

Correct mixed slash and backslash in file path

Convert p-values to lfdr

findSimilFrom2sets

Find similar numeric values from two vectors/matrixes

Fuse annotation matrix to initial matrix

fuseCommonListElem

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

extractLast2numericParts

Extract last two numeric parts from character vector

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

sd for each column

Standard error of median for each column by bootstrap

convColorToTransp

Assign new transparency to given colors

Estimate mode (most frequent value)

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

Standardize (scale) data

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

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

Organize data as separate list-entries

Connect edges to form tree and extract all possible branches

filterLiColDeList

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

Compute matrix of differences for all pairwise combinations of numeric vector

Merge Named Vectors

Filter for unique elements

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

difference in ppm between numeric values

Get all combinations with TRUE from each column

htmlSpecCharConv

Html special character conversion

Number of fragments after cut at specific character(s)

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

Transform (factor) levels into index

findUsableGroupRange

Select groups within given range

cutArrayInCluLike

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

Cut character-vector at multiple sites

Complete list of arrays for same dimensions

Partial unlist of lists of lists

Equal character-length number

Partial distance matrix (focus on closest)

2-factorial limma-style t-test

Filter matrix to keep only first of repeated lines

Make single vector gray-gradient

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

linRegrParamAndPVal

Fit linear regression, return parameters and p-values

Exclude extreme values (based on distance to mean)

Make non-redundant matrix

make MA-List object

Moderated pair-wise t-test from limma

Multiple moderated pair-wise t-tests from limma

getValuesByUnique

Print matrix-content as plot

Convert ulr-name for reading in raw-mode

Replace NAs by low values

Reorganize matrix according to clustering-output

Merge selected columns out of 2 matrix or data.frames

Transform columns of matrix to list of vectors

Calculate all ratios between x and y

Normalize data in various modes

numPairDeColNames

Extract pair of numeric values from vector or column-names

Convert ratio to ppm

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

listBatchReplace

Replacements in list

Reduce table by aggregating smaller groups

sd of median for each row by bootstrap

sd for each row (fast execution)

regrBy1or2point

Rescaling according to reference data using linear regression.

SEM for each row

nonAmbiguousMat

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

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

listGroupsByNames

Organize values into list and sort by names

sampNoDeMArrayLM

Locate sample index from index or name of pair-wise comparisons in list or MArrayLM-object

Filter nodes & edges for extracting networks This function allows extracting and filtering network-data based on fixed threshold () and add sandwich-nodes (nodes inter-connecting initial nodes) out of node-based queries.

firstOfRepLines

Reduce to first occurance of repeated lines

Find close numeric values between two vectors

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

firstOfRepeated

Find first of repeated elements

Pairwise x,y combinations

treatTxtDuplicates

Locate duplicates in text and make non-redundant

t.test on all individual values against all other values

Print matrix-content as plot

Minimum distance/difference between values

nonAmbiguousNum

make numeric vector non-ambiguous (ie unique)

Run lm on segmented data (from clustering)

multiCharReplace

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

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

Non-redundant lines of matrix

nonredDataFrame

Filter for unique elements

rankToContigTab

Contingenty tables for fit of ranking

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

Read tabular content of files with variable number of columns

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

Read batch of Excel xlsx-files

System-date (compressed format)

sortBy2CategorAnd1IntCol

Sort matrix by two categorical and one integer columns

singleLineAnova

2-factorial Anova on single line of data

regrMultBy1or2point

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

uniqCountReport

Report number of unique and redundant elements (optional figure)

(upper) pairwise x,y combinations

Count number of non-numeric characters

CV of replicate plates (list of matrixes)

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

Write (and convert) csv files

Check for values within range of reference

Filter lines of matrix for max number of NAs

Advanced paste-collapse

Read batch of csv-files

readTabulatedBatch

Btach reading of tabulated (text-) files This function allows batch reading of tabulated text files. The files can be designed specifically, alternatively all files from a given directory can be read. If package data.table is

Count number of NAs per row and group of columns

Per line and per group sd-values

Scale data to given minimum and maxiumum

searchDataPairs

Search duplicated data over multiple columns, ie pairs of data

Standard eror of median by boot-strap

Count number of NAs per sub-set of columns