vignette {VariantTools} | R Documentation

## 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)

[Package VariantTools version 1.26.0 Index]