samples_filter: Filter out samples of a vcfR object based on depth

In Neato-Nick/mllR:

Description

Filter out samples of a vcfR object based on depth

Usage

samples_filter(x, lower_quant = 0.05, stat = "median", filter_bot = TRUE,
  filter_top = FALSE, remove_nonpolymorphs = TRUE)

Arguments

x	A vcfR object
lower_quant	lower quantile to filter by. The top quantile will be 1-lower_quant
stat	Statistic to filter by. Right now, supports "median" to filter on median depth, "mean" to filter on mean depth, or "missingness" to filter on percent missing data.
filter_bot	Omit samples in the bottom quantile
filter_top	Omit samples in the top quantile
remove_nonpolymorphs	After omitting samples, some variants will be nonpolymorphic. These should be removed.

Value

A filtered vcfR object.

Examples

ultrafiltered_vcf <- samples_filter(filtered_vcf)

Neato-Nick/mllR documentation built on May 17, 2019, 6:22 p.m.