VariantExplorer: VariantExplorer

In BrentLab/brentlabRnaSeqTools: Management/QC for brentlab RNAseq data

VariantExplorer

Description

Use this to coordinate the analysis of the snpEff summary, alignment files and bam files.

Usage

create_variant_explorer(sample_metadata, gff_ranges, bsgenome, igv_genome = "")

## S4 method for signature 'VariantExplorer'
igv_script(
  x,
  locus,
  output_dir = getwd(),
  image_basename = "",
  exit_browser = TRUE,
  maxPanelHeight = 500,
  ...
)

## S4 method for signature 'VariantExplorer'
summary(object)

## S4 method for signature 'VariantExplorer'
visualize(x, gene, sample, plot_type = "pileup")

Arguments

sample_metadata	sample metadata with at least the columns sample_id, snpeff, variant_caller. Suggested columns are bam and vcf.
gff_ranges	the gff for this organism imported with rtracklayer::import()
bsgenome	path to a BSgenome object. KN99 has one – check bioconductor
igv_genome	path to a genome object created by igvtools
x	a VariantExplorer object
object	a VariantExplorer instance
gene	the name of the gene you wish to visualize
sample	the sample_id you wish to see
plot_type	either 'pileup' or 'coverage'. Defaults to 'pileup'

Details

DETAILS

Value

A VariantExplorer object

See Also

character(0) character(0)

Examples

## Not run: 
if(interactive()){
 #EXAMPLE1
 }

## End(Not run)

BrentLab/brentlabRnaSeqTools documentation built on Aug. 20, 2023, 9:22 a.m.