VCFQAParam: User Constructor for class. Call limits are set as default...

Description Usage Arguments Value Examples

View source: R/VCFQAParam.R

Description

User Constructor for class. Call limits are set as default to pass.

Usage

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VCFQAParam(homref.limits = c(-Inf, Inf), het.limits = c(-Inf, Inf),
  homvar.limits = c(-Inf, Inf), percenthets.limits = c(-Inf, Inf),
  titv.noncoding.limits = c(-Inf, Inf), titv.coding.limits = c(-Inf, Inf),
  readdepth.target = -1, readdepth.limits = c(-Inf, Inf),
  readdepth.percent.limits = 0, gq.limit = 0, masked.limits = c(-Inf,
  Inf), non.masked.limits = c(-Inf, Inf), het.gap.limits = rep(Inf, 24),
  count.limits = c(-Inf, Inf), gq.filter = 0, dp.filter = -1)

Arguments

homref.limits

lower limit, upper limit, number of homozygous reference

het.limits

lower limit, upper limit, number of heterozygous calls

homvar.limits

lower limit, upper limit, number of homozygous alternative

percenthets.limits

lower limit, upper limit, Number of Heterozgyous / (Total Number of Counts) or percent het

titv.noncoding.limits

lower limit, upper limit, Transition transversion ratio in noncoding regions

titv.coding.limits

lower limit, upper limit, Transition transversion ratio in coding regions

readdepth.target

The sequencing depth target (eg 30x)

readdepth.limits

lower limit, upper limit, Mean read depth

readdepth.percent.limits

lower limit, upper limit, Percent read depth in target (50 percent to 200 percent of target read depth)

gq.limit

lower limit, Mean genotype quality (does not make sense to have an upper limit)

masked.limits

lower limit, upper limit, (Number of heterozygous in self chained regions)/(Total number of heterozygotes)

non.masked.limits

lower limit, upper limit, (Number of heterozygous in non-self chained regions)/(Total number of heterozygotes)

het.gap.limits

lower limit, upper limit, Largest gap within chromosome between two heterozygous calls

count.limits

lower limit, upper limit, total number of counts

gq.filter

filter for the VCF file on genotype quality (eg only GQ > 90)

dp.filter

filter for the VCF file on read depth (eg only DP > 0)

Value

Object of class VCFQAParam

Examples

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vcfparams <- VCFQAParam(count.limits=c(3014580000, Inf), readdepth.target = 30)

Bioconductor-mirror/genotypeeval documentation built on June 1, 2017, 9:43 a.m.