plotAllTwoSampleDistributionCounts {pathVar} | R Documentation |
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.
plotAllTwoSampleDistributionCounts(dat,pvalue_results,perc=c(1/3,2/3),pvalue,plotName)
dat |
|
pvalue_results |
output of |
perc |
numeric |
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. |
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.
A plot of results returned.
Laurence de Torrente, Samuel Zimmerman, Jessica Mar
# 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")