getXCIstate {XCIR} | R Documentation |
Classify X-linked genes between Escape (E), Variable Escape (VE) and Silenced (S)
getXCIstate(xciObj)
xciObj |
A |
A data.table
with genes and their XCI-state.
library(data.table) # Simulated data dtf <- system.file("extdata/data2_vignette.tsv", package = "XCIR") dt <- fread(dtf) xcigf <- system.file("extdata/xcig_vignette.txt", package = "XCIR") xcig <- readLines(xcigf) # Run all models on the data all <- betaBinomXI(dt, xciGenes = xcig) # Simple BetaBinomial model and show histogram of skewing bb <- betaBinomXI(dt, xciGenes = xcig, model = "BB", hist = TRUE) # Plotting fits stoshow <- paste0("sample", c(31, 33, 35, 40)) #interesting samples plotQC(all[sample %in% stoshow], xcig = xcig) # Summarizing results # Sample information samps <- sample_clean(all) # Gene-level predictions xcistates <- getXCIstate(all)