create_black_list: Creates a black list of genomic loci based on a background...

In alkodsi/ctDNAtools: Analyze Circulating Tumor DNA Sequencing Data

Description

The function applies criteria on the background panel to extract the noisy genomic loci. Criteria include minimum number of samples having at least one, at least two, or at least n (n_reads parameter) non-reference allele. Additionally the quantile of mean VAF above which the loci are considered noisy

Usage

create_black_list(
  background_panel,
  mean_vaf_quantile = 0.95,
  min_samples_one_read = max(2, ceiling(ncol(background_panel$vaf) * 0.75)),
  min_samples_two_reads = max(2, ceiling(ncol(background_panel$vaf) * 0.2)),
  min_samples_n_reads = NA,
  n_reads = NA
)

Arguments

background_panel	A list produced by create_background panel function
mean_vaf_quantile	The quantile of mean VAF above which the loci are considered noisy. Use NA to skip this criterion.
min_samples_one_read	Loci that at least this number of samples exhibit at least one non-reference reads are considered noisy. Use NA to skip this criterion.
min_samples_two_reads	Loci that at least this number of samples exhibit at least two non-reference reads are considered noisy. Use NA to skip this criterion.
min_samples_n_reads	Loci that at least this number of samples exhibit at least n non-reference reads (n_reads parameter) are considered noisy. Use NA to skip this criterion.
n_reads	the number of reads to use in the min_samples_n_reads parameter

Value

a character vector of the loci in the black list

See Also

create_background_panel test_ctDNA

Examples

## Load example data
data("targets", package = "ctDNAtools")
bamN1 <- system.file("extdata", "N1.bam", package = "ctDNAtools")
bamN2 <- system.file("extdata", "N2.bam", package = "ctDNAtools")
bamN3 <- system.file("extdata", "N3.bam", package = "ctDNAtools")

## Use human reference genome from BSgenome.Hsapiens.UCSC.hg19 library
suppressMessages(library(BSgenome.Hsapiens.UCSC.hg19))

## Use a black list based on loci
bg_panel <- create_background_panel(
  bam_list = c(bamN1, bamN2, bamN3),
  targets = targets, reference = BSgenome.Hsapiens.UCSC.hg19,
  substitution_specific = FALSE
)

bl1 <- create_black_list(bg_panel,
  mean_vaf_quantile = 0.99,
  min_samples_one_read = 2, min_samples_two_reads = 1,
  min_samples_n_reads = 1, n_reads = 3
)

## Use a substitution-specific black list
bg_panel <- create_background_panel(
  bam_list = c(bamN1, bamN2, bamN3),
  targets = targets, reference = BSgenome.Hsapiens.UCSC.hg19,
  substitution_specific = TRUE
)

bl2 <- create_black_list(bg_panel,
  mean_vaf_quantile = 0.99,
  min_samples_one_read = 2, min_samples_two_reads = 1,
  min_samples_n_read = NA
)

alkodsi/ctDNAtools documentation built on Feb. 22, 2022, 9:40 a.m.