telom_centrom {CNVgears}R Documentation

Generate blacklist for telomeric and centromeric regions

Description

Generate blacklist for telomeric and centromeric regions

Usage

telom_centrom(DT_in, telom = TRUE, centrom = TRUE, region = 50000)

Arguments

DT_in,

a data.table with start, and centromere position for each chromosome. For the assemblies hg18, hg19 and hg38 this is provided in the package.

telom,

logical, should be telomeric blacklist be produced?

centrom,

logical, should be centromeric blacklist be produced?

region,

integer. How many basepairs large should the regions be? The centromeric region will be twice this large.

Value

, a data.table that can be passed to cleaning_filter as blacklist.

Examples

DT <- telom_centrom(hg19_start_end_centromeres)

[Package CNVgears version 1.2.0 Index]