removeUnwantedVariants: Remove variants from gnomAD CSV that don't pass filters

In SandersKM/MendelianVariants:

Description

Takes in a CSV of variants from gnomAD, as well as optional filters for annotations and flags. Returns a data frame with the variants that don't contain the filters and flags

Usage

removeUnwantedVariants(df, unwanted_annotations = c("splice region", "synonymous", "3' UTR", "5' UTR", "downstream gene","intron", "upstream gene", "non coding transcript exon"),
unwanted_flags = c("SEGDUP", "LC LoF"))

Arguments

df	Data frame of the gnomAD CSV
unwanted_annotations	Vector containing gnomAD variant annotations that should be filtered out.
unwanted_flags	Vector containing gnomAD flags that should be filtered out.

Value

A data frame containing variants that passed the flag and variant filters

Author(s)

Kate Sanders

References

http://gnomad.broadinstitute.org

Examples

data("MUC1_variants")
cleanVariants <- removeUnwantedVariants(MUC1_variants)

SandersKM/MendelianVariants documentation built on May 12, 2019, 4:35 a.m.