pSI (version 1.1)

pSI.count: Convert pSI output to gene count list

Description

pSI.count This functions counts number of genes specific to each sample type

Usage

pSI.count(pSIs, write.csv = FALSE)

Arguments

pSIs

data frame output from specificity.index function with the number of columns equal to the number of samples and genes as rows.

write.csv

logical variable indicating if csv files will be written to the current working directory (default value is FALSE)

Details

Returns data frame consisting of 6 rows, one for each pSI threshold, and as many columns as cell types/samples were included in the analysis. Each cell type/sample will have a count of many genes whose pSI values fall below each respective threshold for each cell type/sample. NOTE:Supplementary data (human & mouse expression sets, calculated pSI datasets, etc.) can be found in pSI.data package located at the following URL: http://genetics.wustl.edu/jdlab/psi_package/

Examples

##load sample pSI output
data(sample.data)
##Count the number of genes specific to each cell type/sample type across all pSI thresholds
pSI.out.count <- pSI.count(pSIs=sample.data$pSI.output, write.csv=TRUE)