Obtain LOH on an entire chromsomes from samples in a cohort
Usage
lohSpec_lohCalc(window_data, out, normal)
Arguments
window_data
object of class data frame with columns
'window_start' and 'window_stop
out
object of class dataframe with columns 'chromosome',
'position', 'n_vaf', 't_vaf', and 'sample'
normal
integer specifying the subtraction value from tumor VAF
Value
object of class dataframe containing mean LOH difference calculations
and column names "window_start", "window_stop", "chromosome", "position",
"n_vaf", "t_vaf", "sample", "loh_diff"