GoldDataParam: User Constructor for class

In jentom/genotypeeval: QA/QC of a gVCF or VCF file

Description

User Constructor for class

Usage

GoldDataParam(titv.coding.confirmed.l = 0, titv.coding.confirmed.u = 5,
  titv.noncoding.confirmed.l = 0, titv.noncoding.confirmed.u = 5,
  titv.coding.unconfirmed.l = 0, titv.coding.unconfirmed.u = 5,
  titv.noncoding.unconfirmed.l = 0, titv.noncoding.unconfirmed.u = 5,
  percent.confirmed.limits = 0, percent.het.rare.limits = 0)

Arguments

titv.coding.confirmed.l	Lower limit of transition transversion ratio in coding confirmed
titv.coding.confirmed.u	upper limit of transition transverion ratio coding confirmed
titv.noncoding.confirmed.l	Lower limit of transition transversion ratio in noncoding confirmed
titv.noncoding.confirmed.u	upper limit of transition transverion ratio noncoding confirmed
titv.coding.unconfirmed.l	Lower limit of transition transversion ratio in coding unconfirmed
titv.coding.unconfirmed.u	upper limit of transition transverion ratio coding unconfirmed
titv.noncoding.unconfirmed.l	Lower limit of transition transversion ratio in noncoding unconfirmed
titv.noncoding.unconfirmed.u	upper limit of transition transverion ratio noncoding unconfirmed
percent.confirmed.limits	lower limit, upper limit, percent confirmed in Gold comparator
percent.het.rare.limits	lower limit, upper limit, (Percent Het in Rare, MAF < 0.01 in Gold) / Total number of Heterozygotes

Value

Object of type GoldDataParam

Examples

gparam <- GoldDataParam(percent.confirmed=0.792, percent.het.rare = 0.93)

jentom/genotypeeval documentation built on May 13, 2019, 12:54 p.m.