Group of R functions to identify genes specific to a given cell type or condition. These functions compute specificity scores for each gene using all replicates of a given cell type/condition and use permutations to perform statistical testing.
To use these functions, install the proteogenomic package using the following commands:
install.packages("devtools") #If not yet installed
devtools::install_github("eddiecg/proteogenomic")
Proteogenomic contains two main functions:
getSpecificities()
Computes specificity scores but does no statistical testing
testSpecificities()
Computes specificity scores and infers statistical significance via permutations. Also, corrects for multiple hypothesis testing using the Benjamini-Hochberg method