GenVisR (version 1.0.4)

lohSpec_slidingWindow: Obtain LOH data

Description

Obtain LOH heatmap on entire chromsomes from samples in a cohort

Usage

lohSpec_slidingWindow(loh_data, step, window_size, normal)

Arguments

loh_data

data frame with columns "chromosome", "position", "n_vaf", "t_vaf", "sample" giving raw vaf calls for germline variants

step

integer with the length of divisions (bp) in chromosomes

window_size

integer with the size of the sliding window (bp) to be applied

normal

integer specifying the normal VAF frequency used in LOH calculations

Value

object of class dataframe containing LOH data