gene_exon: Get exons for set of genes

Description Usage Arguments Value Author(s) Examples

Description

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

Match up exon start,stop,strand with genes.

Returns table of gene and its exons.

Usage

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get_gene_exon_snp(top_snps_tbl, feature_tbl = query_genes(chr_id,
  range_Mbp[1], range_Mbp[2]))

get_gene_exon(feature_tbl, gene_snp)

## S3 method for class 'gene_exon'
summary(gene_exon, gene_name = NULL,
  top_snps_tbl = NULL, extra = 0.005)

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

Arguments

top_snps_tbl

table from top_snps

feature_tbl

table of features from query_genes; see create_gene_query_func

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

extra region beyond gene for SNPs (in Mbp)

feature_tbl

tbl of features from query_variants; see create_variant_query_func

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, [email protected]

Brian S Yandell, [email protected]

Brian S Yandell, [email protected]

Examples

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## Not run: get_gene_exon_snp(top_snps_tbl)

## Not run: get_gene_exon(feature_snp)

byandell/qtl2pattern documentation built on May 13, 2019, 9:51 a.m.