plotAllTwoSampleDistributionCounts: Compares the distribution of genes in clusters for every gene...

Description Usage Arguments Details Value Author(s) Examples

View source: R/pipeline.final.R

Description

Compares the distribution of genes for every gene in your data set for two groups of samples that you define and plot the counts of each gene.

Usage

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plotAllTwoSampleDistributionCounts(dat,pvalue_results,perc=c(1/3,2/3),pvalue,plotName)

Arguments

dat

matrix with the genes on the rows and the samples on the columns.

pvalue_results

output of pathVarTwoSamples step.

perc

numeric vector of probabilities with values between 0 and 1. Used to put genes into clusters

pvalue

the significance level to test.

plotName

a string specifying the file name of the output plot. Default value is NULL which prints, but does not save the graph in a pdf.

Details

This function looks at the gene counts in each category of 2 groups previously defined in the pathVarTwoSamples step and compare the 2 samples to each other with all the genes from the data set. Then it plots the counts for each group.

Value

A plot of results returned.

Author(s)

Laurence de Torrente, Samuel Zimmerman, Jessica Mar

Examples

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# we run the 2 samples analysis on the first 10 pathways from kegg
pways.kegg.10pways <- lapply(pways.kegg, function(x) x[1:10])
results_2samples=pathVarTwoSamplesDisc(bock,pways.kegg.10pways,groups=as.factor(c(rep(1,10),rep(2,10))),perc=c(1/3,2/3),test="exact",varStat="sd")
plotAllTwoSampleDistributionCounts(bock, results_2samples, perc=c(1/3,2/3), pvalue=0.05, "bock.group1.group2.pdf")

jmarlab/pathVar documentation built on May 23, 2019, 9:02 p.m.