checkMarkers {fbat} | R Documentation |
Basic data quality checks for markers.
checkMarkers(geneSetObj, founderOnly=TRUE, thrsh=0.05, quiet=TRUE)
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 . |
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. |
Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus ross.lazarus@channing.harvard.edu
data(CAMP) res<-checkMarkers(CAMP) print(res)