checkMarkers {fbat}R Documentation

Basic data quality checks for markers

Description

Basic data quality checks for markers.

Usage

checkMarkers(geneSetObj, founderOnly=TRUE, thrsh=0.05, quiet=TRUE)

Arguments

geneSetObj a geneSet object.
founderOnly indicates if using only founder info
thrsh threshold for Hardy-Weinberg test. If the pvalue of the HW test for a marker is greater than thrsh, then the marker is a good marker.
quiet print intermediate results if quiet=FALSE.

Value

a data frame contains components:

Name marker names.
Position marker positions.
ObsHET marker's observed heterozygosity (i.e., proportion of heterozygotes at markes). Missing alleles are excluded in the calculation.
PredHET marker's predicted heterozygosity (i.e., 2*MAF*(1-MAF)). Missing alleles are excluded in the calculation.
HWpval pvalues for Hardy-Weinberg test
pGeno percentage of non-missing genotypes for markes
MAF minor allele frequencies. missing allele are excluded from calculation
Rating Rating[i]=1 means that the $i$-th marker passes HW test (do not reject H0 that HW equilibrium holds). Rating[i]=0 means HW equilibrum does hold for the $i$-th marker.

Author(s)

Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus ross.lazarus@channing.harvard.edu

Examples

  data(CAMP)
  res<-checkMarkers(CAMP)
  print(res)

[Package fbat version 1.0.0 Index]