R/get_mutations_read_counts.R
get_mutations_read_counts.RdCounts ref and alt reads for a set of mutations in a bam file
get_mutations_read_counts(mutations, bam, tag = "", min_base_quality = 20, max_depth = 1e+05, min_mapq = 30)
| mutations | A data frame with the reporter mutations. Should have the columns CHROM, POS, REF, ALT. |
|---|---|
| bam | path to bam file |
| tag | the RG tag if the bam has more than one sample |
| 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 |
a named list contains: ref, vector of read counts of the reference alleles, and alt, vector of read counts of the alternative allele
Quantifies the reference and variant alleles for the input mutations in the input bam file. Useful for forced calling mutations.
get_mutations_read_names test_ctDNA get_mutations_fragment_size
data("mutations", package = "ctDNAtools") bamT1 <- system.file("extdata", "T1.bam", package = "ctDNAtools") get_mutations_read_counts(mutations = mutations[1:3, ], bam = bamT1)#> $ref #> [1] 445 447 373 #> #> $alt #> [1] 2 3 1 #>