Export DiffSegR Results

For each locus, exportResults() saves DERs, not-DERs, segmentation, coverage profiles and Log2-FC per-base in formats readable (bedGraph,GFF3) by genome viewers like the Integrative Genome Viewer (IGV). For IGV, export also creates an IGV sessiong in XML that allows loading all tracks in one click. exportResults() can operate on each locus in parallel.

Usage

exportResults(
  data,
  features,
  sizeFactors,
  outputDirectory,
  genome,
  annotations = NA,
  igvVersion = "8",
  select = c(),
  verbose = TRUE
)

Arguments

data

The List object returned by newExperiment().

features

The GRanges part of the object returned by dea().

sizeFactors

A numericvector of normalization factors for samples.`

outputDirectory

A String. Path to the output directory. One directory by locus will be create within outputDirectory.

genome

A String. Path to the genome on which reads have been aligned.

annotations

A String. Path to the annotation file.

igvVersion

A String. What IGV version should be used in the XML file.

select

A vector of String. Additional information that appear for each region in IGV. only columns from features matching these names are kept.

verbose

A Logical. Should all the operations performed be displayed ?