sig.hets: Identify significantly different heterozygotes from SNPs data

In rCNV: Detect Copy Number Variants from SNPs Data

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,
  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(s)

Piyal Karunarathne, Pascal Milesi, Klaus Schliep, Qiujie Zhou

Examples

## Not run: data(alleleINF)
AI <- alleleINF
duplicates<-sig.hets(AI,plot=TRUE,Fis=0.1)
## End(Not run)

rCNV documentation built on Sept. 30, 2024, 9:39 a.m.