snpeff: Browse Variant Info

Description Usage Arguments Value Examples

Description

snpeff enables you to query variants called and annotated by the Andersen Lab.

Usage

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snpeff(..., severity = c("HIGH", "MODERATE"), elements = c("exon"),
  long = TRUE, remote = FALSE, vcf = NA)

Arguments

...

Gene names, regions, or wormbase identifiers to query.

severity

A vector with variants of given severities (LOW, MODERATE, HIGH, MODIFIER). Default takes moderate and high. Use "ALL" to return all variants.

elements

A vector containing gene structural elements (CDS, five_prime_UTR, exon, intron, three_prime_UTR). Use "ALL" to return all variants.

long

Return dataset in long or wide format. Default is to return in long format.

remote

Use remote data. Checks for local data if possible. False by default.

use

custom vcf file.

Value

Outputs a data frame that contains phenotype data, mapping data, and gene information for highly correlated variants in a particular QTL confidence interval.

Examples

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snpeff("pot-2","II:1-10000","WBGene00010785")

AndersenLab/cegwas documentation built on March 6, 2020, 1:10 a.m.