GenVisR (version 1.0.2)

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