calculateMappingBiasVcf {PureCN} | R Documentation |
Function calculate mapping bias for each variant in the provided panel of normals VCF.
calculateMappingBiasVcf( normal.panel.vcf.file, min.normals = 1, min.normals.betafit = 7, min.normals.assign.betafit = 3, min.normals.position.specific.fit = 10, min.median.coverage.betafit = 5, num.betafit.clusters = 9, min.betafit.rho = 1e-04, max.betafit.rho = 0.2, yieldSize = 50000, genome )
normal.panel.vcf.file |
|
min.normals |
Minimum number of normals with heterozygous SNP for calculating position-specific mapping bias. |
min.normals.betafit |
Minimum number of normals with heterozygous SNP fitting a beta binomial distribution |
min.normals.assign.betafit |
Minimum number of normals with heterozygous SNPs to assign to a beta binomal fit cluster |
min.normals.position.specific.fit |
Minimum normals to use position-specific beta-binomial fits. Otherwise only clustered fits are used. |
min.median.coverage.betafit |
Minimum median coverage of normals with heterozygous SNP for fitting a beta binomial distribution |
num.betafit.clusters |
Maximum number of beta binomial fit clusters |
min.betafit.rho |
Minimum dispersion factor rho |
max.betafit.rho |
Maximum dispersion factor rho |
yieldSize |
See |
genome |
See |
A GRanges
object with mapping bias and number of normal
samples with this variant.
Markus Riester
normal.panel.vcf <- system.file("extdata", "normalpanel.vcf.gz", package = "PureCN") bias <- calculateMappingBiasVcf(normal.panel.vcf, genome = "h19") saveRDS(bias, "mapping_bias.rds")