vignette | R Documentation |
Precomputed data for use in the vignette, mostly for the sake of Windows, where gmapR and its tallying functionality are unsupported.
data(vignette)
The following objects are included:
Tallies for the two samples.
Coverage for the two samples.
A GRanges of the p53 exons
DNAStringSet with the genome sequence of the p53 region
The following demonstrates how we created these objects:
bams <- LungCancerLines::LungCancerBamFiles() tally.param <- TallyVariantsParam(gmapR::TP53Genome(), high_base_quality = 23L, which = range(p53) + 5e4, indels = TRUE, read_length = 75L) tallies_H1993 <- tallyVariants(bams$H1993, tally.param) tallies_H2073 <- tallyVariants(bams$H2073, tally.param) coverage_H1993 <- coverage(bams$H1993) coverage_H2073 <- coverage(bams$H2073) genome_p53 <- DNAStringSet(getSeq(gmapR::TP53Genome())) p53 <- gmapR:::exonsOnTP53Genome("TP53")
Computed from the data in the LungCancerLines package.
data(vignette)
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