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)
checkMarkers.default(pedObj, founderOnly=TRUE, thrsh=0.05, quiet=TRUE)

Arguments

geneSetObj a geneSet object.
pedObj a list with five elements: ped, columns, markerNames, Position, and filename. ped is a pedigree data frame whose first 6 columns are family (pedigree id), pid (patient id), father (father id), mother (mother id), sex, affected (affection status). The remaining columns are pairs of marker alleles. Each row corresponds to an individual; columns are the names of the first 5 (or 6) columns of ped file. It should be either equal to c("family","pid","father","mother","sex","affected") or equal to c("family","pid","father","mother","sex"); founderOnly indicates if using only founder info; markerNames is a vector of marker names; Position is a vector of marker positions; fileName is the pedigree file name
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, Gregory Warnes warnes@bst.rochester.edu, Nitin Jain nitin.jain@pfizer.com

Examples

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

[Package fbat version 1.2.0 Index]