# Get exons for set of genes 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. ```r 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$gene), ... ) ## S3 method for class 'gene_exon' autoplot(object, ...) ``` ## Arguments - `top_snps_tbl`: table from `top_snps` - `feature_tbl`: table of features from `query_genes`; see `create_gene_query_func` - `object`: Object of class `gene_exon`. - `gene_name`: name of gene as character string - `extra`: extra region beyond gene for SNPs (in Mbp) - `...`: arguments passed along to `gene_exon` - `x`: Object of class `gene_exon`. - `gene_val`: Name of gene from object `x`. - `plot_now`: plot now if TRUE - `genes`: Names of genes in `object` ## Returns tbl of exon and gene features tbl of summary list of ggplots (see `gene_exon`) ## Examples ```r dirpath <- "https://raw.githubusercontent.com/rqtl/qtl2data/master/DOex" # Read DOex example cross from 'qtl2data' DOex <- subset(qtl2::read_cross2(file.path(dirpath, "DOex.zip")), chr = "2") # Download genotype probabilities tmpfile <- tempfile() download.file(file.path(dirpath, "DOex_genoprobs_2.rds"), tmpfile, quiet=TRUE) pr <- readRDS(tmpfile) unlink(tmpfile) # Download SNP info for DOex from web and read as RDS. tmpfile <- tempfile() download.file(file.path(dirpath, "c2_snpinfo.rds"), tmpfile, quiet=TRUE) snpinfo <- readRDS(tmpfile) unlink(tmpfile) snpinfo <- dplyr::rename(snpinfo, pos = pos_Mbp) # Convert to SNP probabilities snpinfo <- qtl2::index_snps(DOex$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]) ``` ## Author(s) Brian S Yandell, brian.yandell@wisc.edu

gene_exon function