isNotGermline: Assess whether a region can be attributable to a germline CNV...

In cancer-genomics/trellis: Somatic structural variant analysis

Assess whether a region can be attributable to a germline CNV or artifact seen in germline samples

Description

In our application, all_filters is a GRanges object comprised of germline CNVs and sequence filters. The latter is a collection of 1kb bins (reduced) that have low mappability (< 0.75) and/or low GC content (< 0.1). For each interval in the candidate somatic GRanges object (g), we compute the fraction of the interval spanned by the germline filters. If the fraction of the candidate somatic variant spanned by the germline filter is less than max_proportion_in_filter AND the width not spanned by the germline filters is less than min_width, this function evaluates to TRUE.

Usage

isNotGermline(g, all_filters, param = DeletionParam())

Arguments

g	a GRanges object (e.g., candidate deletions)
all_filters	a GRanges object (e.g., deletions, amplifications, and outliers identified in the germline)
param	an instance of DeletionParam

Value

a locical vector having the same length as g

See Also

See DeletionParam for default values of max_proportion_in_filter and min_width.

cancer-genomics/trellis documentation built on Feb. 2, 2023, 7:04 p.m.