test_exon_gr: Sample exon data GRanges

In jmw86069/splicejam: Analysis and Visualization of Gene Splice Variants and Transcriptome Data

Sample exon data GRanges

Description

Sample exon data GRanges

Usage

test_exon_gr

Format

GRanges object where each segment represents one exon for an arbitrary gene. It has one column of values, "gene_name" used for Sashimi plot preparation.

Details

This dataset contains RNA-seq splice junction data stored as a GRangesList.

See Also

Other splicejam data: test_cov_gr, test_cov_wide_gr, test_exon_wide_gr, test_junc_gr, test_junc_wide_gr

Examples

# The code below is used to create the exon test data
suppressPackageStartupMessages(library(GenomicRanges));
suppressPackageStartupMessages(library(ggplot2));

test_exon_gr <- GRanges(seqnames=rep("chr1", 4),
   ranges=IRanges::IRanges(
      start=c(100, 300, 500, 900),
        end=c(199, 399, 749, 999)),
   strand=rep("+", 4),
   gene_name=rep("TestGene1", 4));
names(test_exon_gr) <- jamba::makeNames(rep("exon", length(test_exon_gr)),
   suffix="");

# To plot a simple GRanges object
ggplot(grl2df(test_exon_gr), aes(x=x, y=y, group=id, fill=feature_type)) +
   geom_polygon() +
   colorjam::theme_jam() +
   colorjam::scale_fill_jam()

jmw86069/splicejam documentation built on Nov. 4, 2024, 10:53 a.m.