pSI (version 1.1)

pSI.list: Convert pSI output to gene list

Description

pSI.list returns list consisting of 6 data frames, one for each pSI threshold.

Usage

pSI.list(pSIs, write.csv = TRUE)

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

Each data frame contains genes whose pSI values fall below each respective threshold for each cell type/sample included in the analysis. 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)
##List the genes specific to each cell type/sample type across all pSI thresholds
pSI.out.list <- pSI.list(pSIs=sample.data$pSI.output, write.csv=FALSE)