sig.hets {rCNV} | R Documentation |
Identify significantly different heterozygotes from SNPs data
Description
This function will recognize the SNPs with a proportion of heterozygotes significantly higher than expected under HWE and plot deviant snps based only on the excess of heterozygotes.
Usage
sig.hets(
a.info,
method = c("chi.sq", "fisher"),
plot = TRUE,
verbose = TRUE,
...
)
Arguments
a.info |
allele info table generated from filtered vcfs using the
function |
method |
character. Method for testing significance. Fisher exact test
( |
plot |
logical. Whether to plot the identified duplicated snps with the expected values |
verbose |
logical, if TRUE, the progress is shown |
... |
other arguments passed to |
Value
A matrix of expected heterozygote proportions from the observed data with p-value indicating significance of deviation.
Author(s)
Piyal Karunarathne, Pascal Milesi, Klaus Schliep
Examples
## Not run: data(alleleINF)
AI <- alleleINF
duplicates<-sig.hets(AI,plot=TRUE)
## End(Not run)
[Package rCNV version 1.2.0 Index]