# Plot of merge_feature object Merge all SNPs in small region with LOD peaks across multiple phenotype. ```r ggplot_merge_feature(object, pheno, plot_by = c("pattern", "consequence"), ...) ## S3 method for class 'merge_feature' autoplot(object, ...) merge_feature( top_snps_tbl, snpinfo, out_lmm_snps, drop = 1.5, dropchar = 0, exons = gene_exon(top_snps_tbl) ) ## S3 method for class 'merge_feature' summary(object, sum_type = c("SNP type", "pattern"), ...) ``` ## Arguments - `object`: of class `merge_feature` - `pheno`: name of phenotype to be plotted - `plot_by`: element to plot by (one of `c("pattern","consequence")`) - `...`: other arguments not used - `top_snps_tbl`: tbl from `top_snps_pattern` or `top_snps` - `snpinfo`: SNP information table - `out_lmm_snps`: tbl from `scan1` on SNPs - `drop`: include LOD scores within `drop` of max for each phenotype - `dropchar`: number of characters to drop on phenames - `exons`: table from `gene_exon` - `sum_type`: one of `c("SNP type","pattern")` ## Returns ggplot2 object tbl with added information on genes and exons table summary ## 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) summary(top_snps_tbl) # 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) out <- merge_feature(top_snps_tbl, snpinfo, scan_snppr, exons = gene_tbl) summary(out, "pattern") ``` ## Author(s) Brian S Yandell, brian.yandell@wisc.edu

merge_feature function