vignette: Vignette Data

In lawremi/VariantTools: Tools for Exploratory Analysis of Variant Calls

Vignette Data

Description

Precomputed data for use in the vignette, mostly for the sake of Windows, where gmapR and its tallying functionality are unsupported.

Usage

data(vignette)

Format

The following objects are included:

tallies_H1993, tallies_H2073

Tallies for the two samples.

coverage_H1993, coverage_H2073

Coverage for the two samples.

p53

A GRanges of the p53 exons

genome_p53

DNAStringSet with the genome sequence of the p53 region

Details

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")
  

Source

Computed from the data in the LungCancerLines package.

Examples

data(vignette)

lawremi/VariantTools documentation built on March 4, 2024, 11:54 a.m.