gene_exon {qtl2pattern}

Get exons for set of genes

Description

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

Returns table of gene and its exons.

Uses gene_exon to plot genes, exons, mRNA with SNPs.

Usage

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

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

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

ggplot_gene_exon(
  object,
  top_snps_tbl = NULL,
  plot_now = TRUE,
  genes = unique(object$gene),
  ...
)

## S3 method for class 'gene_exon'
autoplot(object, ...)

Arguments

top_snps_tbl

table from top_snps

feature_tbl

table of features from query_genes; see create_gene_query_func

object

Object of class gene_exon.

gene_name

name of gene as character string

extra

extra region beyond gene for SNPs (in Mbp)

...

arguments passed along to gene_exon

x

Object of class gene_exon.

gene_val

Name of gene from object x.

plot_now

plot now if TRUE

genes

Names of genes in object

Value

tbl of exon and gene features

tbl of summary

list of ggplots (see gene_exon)

Author(s)

Brian S Yandell, [e-mail]

Examples

dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex"

# Read DOex example cross from 'qtl2data'
DOex <- subset(qtl2::read_cross2(file.path(dirpath, "DOex.zip")), chr = "2")


# Download genotype probabilities
tmpfile <- tempfile()
download.file(file.path(dirpath, "DOex_genoprobs_2.rds"), tmpfile, quiet=TRUE)
pr <- readRDS(tmpfile)
unlink(tmpfile)

# Download SNP info for DOex from web and read as RDS.
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE)
snpinfo <- readRDS(tmpfile)
unlink(tmpfile)
snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp)

# Convert to SNP probabilities
snpinfo <- qtl2::index_snps(DOex$pmap, snpinfo)
snppr <- qtl2::genoprob_to_snpprob(pr, snpinfo)

# Scan SNPs.
scan_snppr <- qtl2::scan1(snppr, DOex$pheno)

# Collect top SNPs
top_snps_tbl <- top_snps_pattern(scan_snppr, snpinfo)

# Download Gene info for DOex from web via RDS
tmpfile <- tempfile()
download.file(file.path(dirpath, "c2_genes.rds"), tmpfile, quiet=TRUE)
gene_tbl <- readRDS(tmpfile)
unlink(tmpfile)

# Get Gene exon information.
out <- gene_exon(top_snps_tbl, gene_tbl)
summary(out, gene = out$gene[1])