filter_snp: Filter SNPs based on the output of 'multidog()'.

In updog: Flexible Genotyping for Polyploids

Filter SNPs based on the output of multidog().

Description

Filter based on provided logical predicates in terms of the variable names in x$snpdf. This function filters both x$snpdf and x$inddf.

Usage

filter_snp(x, expr)

Arguments

x	The output of multidog.
expr	Logical predicate expression defined in terms of the variables in x$snpdf. Only SNPs where the condition evaluates to TRUE are kept.

Author(s)

David Gerard

See Also

multidog():

For the variables in x$snpdf which you can filter by.

Examples

## Not run: 
data("uitdewilligen")
mout <- multidog(refmat = t(uitdewilligen$refmat),
                 sizemat = t(uitdewilligen$sizemat),
                 ploidy = uitdewilligen$ploidy,
                 nc = 2)

## The following filters are for educational purposes only and should
## not be taken as a default filter:
mout2 <- filter_snp(mout, bias < 0.8 & od < 0.003)

## End(Not run)

updog documentation built on Nov. 17, 2023, 9:06 a.m.