Read in CNV profile data.table of various flavors and extract a corrected profile

Given a data.table or GenomicRanges CNV object, extract the corrected CNV profile. Any segment with a non-rounded value within 0.2 of the next integer value is rounded to that value. The output will data.table will contain 6 columns: sample, seqnames, start, end, total, minor The sample is either user-provided or row count placeholder Currently supports CNV calls from Battenberg and FACETS

Usage

get_corrected_cnv_profile(cnv_obj, caller, sample_id = NULL)

Arguments

cnv_obj

CNV file in data.table or GenomicRanges format

caller

Name of caller that generated input CNV to be converted, supported: Battenberg and FACETS

sample_id

Unique identifier to add to output, default: NULL

Value

data.table object with corrected CNV segments