Description Usage Arguments Details Value See Also Examples
View source: R/get_background_rate.R
Runs through the target regions base by base counting the mismatches. Then it divides sum(mismatches)/sum(depths) for all bases in the targets
1 2 3 | get_background_rate(bam, targets, reference, vaf_threshold = 0.1,
tag = "", black_list = NULL, substitution_specific = TRUE,
min_base_quality = 20, max_depth = 1e+05, min_mapq = 30)
|
bam |
path to bam file |
targets |
a data frame with the target regions. Must have three columns: chr, start and end |
reference |
the reference genome in BSgenome format |
vaf_threshold |
the bases with higher than this VAF threshold will be ignored in the calculation (real mutations) |
tag |
the RG tag if the bam has more than one sample |
black_list |
a character vector of genomic loci of format chr_pos if substitution_specific is false, or chr_pos_ref_alt if substitution_specific is true. The background will be computed on the target regions after excluding black_list loci. |
substitution_specific |
logical, whether to have the loci of black_list by substitutions. |
min_base_quality |
minimum base quality for a read to be counted |
max_depth |
maximum depth above which sampling will happen |
min_mapq |
the minimum mapping quality for a read to be counted |
Computes the background rate of the input bam file for all bases in the specified targets. Substitutions-specific rates are also calculated.
Genomic positions having non-reference allele frequency higher than vaf_threshold will be excluded (to exclude SNPs and real mutations).
If a black_list is specified, the positions in the black_list (whether substitution_specific or not) will be excluded before computing the background rate.
a list containing the general mismatch rate and substitution-specific rates
create_black_list
test_ctDNA
create_background_panel
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | ## Load example data
data("targets", package = "ctDNAtools")
bamT1 <- system.file("extdata", "T1.bam", 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))
## basic usage
get_background_rate(bamT1, targets, BSgenome.Hsapiens.UCSC.hg19)
## more options
get_background_rate(bamT1, targets, BSgenome.Hsapiens.UCSC.hg19,
min_base_quality = 30, min_mapq = 40, vaf_threshold = 0.05
)
## with blacklist
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
)
get_background_rate(bamT1, targets, BSgenome.Hsapiens.UCSC.hg19,
black_list = bl2
)
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