setMappingBiasVcf {PureCN} | R Documentation |
Function to set mapping bias for each variant in the provided
CollapsedVCF
object. By default, it returns the same value for all
variants, but a pool of normal samples can be provided for position-specific
mapping bias calculation.
setMappingBiasVcf(vcf, tumor.id.in.vcf = NULL, normal.panel.vcf.file = NULL, min.normals = 2, smooth = TRUE, smooth.n = 5)
vcf |
|
tumor.id.in.vcf |
Id of tumor in case multiple samples are stored in VCF. |
normal.panel.vcf.file |
Combined VCF file of a panel of normals,
reference and alt counts as AD genotype field. Should be compressed and
indexed with bgzip and tabix, respectively. One can provide a precomputed
mapping bias database
(obtained by |
min.normals |
Minimum number of normals with heterozygous SNP for
calculating position-specific mapping bias. Requires
|
smooth |
Impute mapping bias of variants not found in the panel by
smoothing of neighboring SNPs. Requires |
smooth.n |
Number of neighboring variants used for smoothing. |
A list with elements
bias |
A |
pon.count |
A |
Markus Riester
# This function is typically only called by runAbsoluteCN via # fun.setMappingBiasVcf and args.setMappingBiasVcf. vcf.file <- system.file("extdata", "example.vcf.gz", package="PureCN") vcf <- readVcf(vcf.file, "hg19") vcf.bias <- setMappingBiasVcf(vcf)