correlation: Calculates the correlation between sample-wise amounts of...

In TIN: Transcriptome instability analysis

Description

The function makes use of the corAndPValue function from the WGCNA package to calculate sample-wise Pearson correlation between relative amounts of aberrant exon usage and splicing factor expression levels.

Usage

    correlation(splicingFactors, geneSummaries, tra)

Arguments

splicingFactors	A data.frame with a list of splicing factor genes (Affymetrix transcript cluster id's and gene symbols) to be included in the correlation analysis. The list can include any set of genes included in the data.frame returned from the function 'readGeneSummaries'. An example set of 280 genes is obtained by issuing the command 'data(splicingFactors)'.
geneSummaries	A data.frame with gene-level expression values for all samples, returned from the 'readGeneSummaries' function.
tra	List of sample-wise total relative amounts of aberrant exon usage, returned from the 'aberrantExonUsage' function.

Value

A list with sample-wise Pearson correlation values between relative amounts of aberrant exon usage and splicing factor expression levels.

Examples

    data(sampleSetGeneSummaries)
    gs <- sampleSetGeneSummaries
    fs <- firmaAnalysis(useToyData=TRUE)
    tra <- aberrantExonUsage(1.0, fs)
# calculate correlation between splicing factor expression and aberrant
# exon usage
    data(splicingFactors)
    corr <- correlation(splicingFactors, gs, tra)

Example output

Loading required package: data.table
Loading required package: impute
Loading required package: aroma.affymetrix
Loading required package: R.utils
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.22.0 (2018-04-21) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

The following objects are masked from 'package:methods':

    getClasses, getMethods

The following objects are masked from 'package:base':

    attach, detach, gc, load, save

R.utils v2.8.0 successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

The following object is masked from 'package:utils':

    timestamp

The following objects are masked from 'package:base':

    cat, commandArgs, getOption, inherits, isOpen, parse, warnings

Loading required package: aroma.core
Loading required package: R.filesets
R.filesets v2.13.0 successfully loaded. See ?R.filesets for help.

Attaching package: 'R.filesets'

The following objects are masked from 'package:R.utils':

    extract, validate

The following objects are masked from 'package:base':

    append, readLines

Loading required package: R.devices
R.devices v2.16.0 (2018-07-21) successfully loaded. See ?R.devices for help.
aroma.core v3.1.3 (2018-04-29) successfully loaded. See ?aroma.core for help.

Attaching package: 'aroma.core'

The following objects are masked from 'package:base':

    .Machine, colMeans, colSums, library, require, write

Loading required package: aroma.light
aroma.light v3.6.0 (2017-04-14) successfully loaded. See ?aroma.light for help.

Attaching package: 'aroma.light'

The following objects are masked from 'package:aroma.affymetrix':

    averageQuantile, normalizeQuantile, plotDensity, plotMvsA,
    plotXYCurve

The following objects are masked from 'package:aroma.core':

    callNaiveGenotypes, normalizeTumorBoost

Loading required package: affxparser

Attaching package: 'affxparser'

The following object is masked from 'package:aroma.affymetrix':

    writeCdf

The following object is masked from 'package:R.utils':

    findFiles

The following object is masked _by_ package:aroma.affymetrix:

    writeCdf

The following object is masked from package:R.utils:

    findFiles

aroma.affymetrix v3.1.1 (2018-04-05) successfully loaded. See ?aroma.affymetrix for help.

Attaching package: 'aroma.affymetrix'

The following objects are masked _by_ 'package:aroma.light':

    averageQuantile, normalizeQuantile, plotDensity, plotMvsA,
    plotXYCurve

The following object is masked from 'package:affxparser':

    writeCdf

TIN documentation built on Nov. 8, 2020, 5:58 p.m.