getXCIstate: Classify X-genes

In XCIR: XCI-inference

Description

Classify X-linked genes between Escape (E), Variable Escape (VE) and Silenced (S)

Usage

getXCIstate(xciObj)

Arguments

xciObj

A data.table. The table returned by betaBinomXI

Value

A data.table with genes and their XCI-state.

Examples

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)

XCIR documentation built on Nov. 8, 2020, 7:41 p.m.