desMarkers {GeneticsBase}R Documentation

Descriptive statistics for markers

Description

Descriptive statistics for markers.

Usage

desMarkers(geneSetObj,
           founderOnly=TRUE,
           thrsh=0.05,
           HWE.method=c("simulate","exact"),
           simulate.p.value=FALSE,
           B=10000,
           markerThrsh=100,
           maxDist=5,
           LDmeasure="r2",
           plot=TRUE,
           ...)

Arguments

geneSetObj a geneSet object.
founderOnly indicates if using only founder info
thrsh threshold for Hardy-Weinberg equilibrium test. If the pvalue of the HWE test for a marker is greater than thrsh, then the marker is a good marker.
HWE.method method to do Hardy-Weinberg equilibrium test.
simulate.p.value indicates if the pvalue of the HWE test is calculated by Monte Carlo simulation. simulate.p.value=FALSE means the pvalue is calculated from asymptotic chi-squared distribution of the test statistic. Otherwise, Monte Carlo simulation is used to calculate pvalue. For more details, please refers to the R function chisq.test.
B the number of replicates used in Monte Carlo simulation to get the pvalue of HWE test. For more details, please refers to the R function chisq.test.
markerThrsh if the number of markers is greater than this threshold, then 'LDdist' is called instead of 'LD'.
maxDist the width of window used in 'LDdist' function.
LDmeasure indicates if r^2 or D' is to be plot.
plot indicates if LD plot is output or not.
... Other arguments that are used by HWE.chisq or HWE.exact.

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<-desMarkers(CAMP)
  #print(res)

[Package GeneticsBase version 1.2.0 Index]