Sample junction data GRangesList

Sample junction data GRangesList

test_junc_gr

Format

GRangesList where each GRangesList item represents a distinct biological sample. Each GRanges item represents one splice junction, whose score represents the abundance of splice junction reads observed. The start of each splice junction should be one base after the end of the corresponding exon, using 1-based coordinates. Therefore, an exon spanning 1-10 covers 10 bases, the corresponding junction would begin at position 11. Similarly, if the connected exon begins at position 100, the junction would end at position 99.

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_gr, test_exon_wide_gr, test_junc_wide_gr

Examples

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

test_junc_gr <- GRanges(seqnames=rep("chr1", 5),
   ranges=IRanges::IRanges(
      start=c(200, 200, 400, 400, 750),
        end=c(299, 499, 499, 899, 899)),
   strand=rep("+", 5),
   score=c(200, 50, 120, 80, 170),
   sample_id=rep("sample_A", 5));
names(test_junc_gr) <- jamba::makeNames(
   rep("junc", length(test_junc_gr)),
   suffix="");
test_junc_gr;
#> GRanges object with 5 ranges and 2 metadata columns:
#>         seqnames    ranges strand |     score   sample_id
#>            <Rle> <IRanges>  <Rle> | <numeric> <character>
#>   junc1     chr1   200-299      + |       200    sample_A
#>   junc2     chr1   200-499      + |        50    sample_A
#>   junc3     chr1   400-499      + |       120    sample_A
#>   junc4     chr1   400-899      + |        80    sample_A
#>   junc5     chr1   750-899      + |       170    sample_A
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths

# To plot junctions, use grl2df(..., shape="junction")
junc_df <- grl2df(test_junc_gr, shape="junction")
gg1 <- ggplot(junc_df, aes(x=x, y=y, group=id, fill=gr_name)) +
   ggforce::geom_diagonal_wide(alpha=0.7) +
   colorjam::theme_jam() +
   colorjam::scale_fill_jam()
print(gg1);