In CreRecombinase/FGEM: R package for Functional Genomics using Expectation Maximization (FGEM)

knitr::opts_chunk$set(echo = TRUE)

FGEM Data

The Bayes Factors file is:

library(FGEM)
library(readr)
library(dplyr)
datafile <- "~/Dropbox/BayesianDA/FGEM_Data/TADA_ASC_SSC_results_Dec23.csv"
datadf <- read.table(datafile,header=T,sep=",",stringsAsFactors = F)
datadf <- dplyr::select(datadf,Gene,BF)
saveRDS(datadf,"~/Dropbox/BayesianDA/FGEM_Data/TADA.RDS")
genes <- datadf$Gene

The next step is to load the gene ontology dataframe (using the gene list obtained above) We'll start with the "Biological Processes" type of GO term

library(dplyr)
MFGOdf <- GO2df(genes,terms = "MF")
BPGOdf  <- GO2df(genes,terms="BP") 
GOdf <- bind_rows(MFGOdf,BPGOdf)

CreRecombinase/FGEM documentation built on July 17, 2020, 5:30 a.m.