Identify significantly different heterozygotes from SNPs data

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,
  Fis,
  method = c("chi.sq", "fisher"),
  plot = TRUE,
  verbose = TRUE,
  ...
)

Arguments

a.info

allele info table generated from filtered vcfs using the function allele.info or allele depth table generated from hetTgen

Fis

numeric. Inbreeding coefficient calculated using h.zygosity() function

method

character. Method for testing significance. Fisher exact test (fisher) or Chi-square test (chi.sq)

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 plot

Value

A matrix of expected heterozygote proportions from the observed data with p-value indicating significance of deviation.

Author

Piyal Karunarathne, Pascal Milesi, Klaus Schliep, Qiujie Zhou

Examples

if (FALSE) data(alleleINF)
AI <- alleleINF
duplicates<-sig.hets(AI,plot=TRUE,Fis=0.1) # \dontrun{}
#> assessing excess of heterozygotes