desMarkers {GeneticsBase} | R Documentation |
Descriptive statistics for markers.
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, ...)
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. |
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<-desMarkers(CAMP) #print(res)