gene_exon: Get exons for set of genes

In byandell/CCSanger: Utilities to get and use Sanger data for Collaborative Cross

Description

Match up exon start,stop,strand with genes. Use query_genes to find features; see qtl2db.

Match up exon start,stop,strand with genes.

Returns table of gene and its exons.

Usage

get_gene_exon_snp(top_snps_tbl)

get_gene_exon(feature_tbl, gene_snp)

## S3 method for class 'gene_exon'
summary(gene_exon, gene_name = NULL,
  top_snps_tbl = NULL, extra_bp = 5000)

## S3 method for class 'gene_exon'
subset(x, gene_val, ...)

Arguments

top_snps_tbl	table from top_snps
feature_tbl	tbl of features from query_variants; see package qtl2db
gene_snp	tbl of genes with SNPs IDs from match_feature_snp
gene_exon	tbl of feature information from get_gene_exon
gene_name	name of gene as character string
extra_bp	extra region beyond gene for SNPs (in bp)
top_snps_tbl	table of top SNPs in region from top_snps

Value

tbl of exon and gene features

tbl of exon and gene features

tbl of summary

Author(s)

Brian S Yandell, [e-mail]

Brian S Yandell, [e-mail]

Brian S Yandell, [e-mail]

Examples

## Not run: get_gene_exon_snp(top_snps_tbl)

## Not run: get_gene_exon(feature_snp)

byandell/CCSanger documentation built on May 13, 2019, 9:26 a.m.