Annotate: Annotation of segmented regions and generation of an HTML QC...

In gustaveroussy/EaCoN: EaCoN : Easy Copy Number !

Description

This function performs the genomic annotation of segmented regions, and builds an HTML interactive QC report.

Usage

  Annotate(data = NULL, refGene.table = NULL, targets.table = NULL,
  report = TRUE, author.name = "", out.dir = getwd())

Arguments

data	Data object contained in a RDS file generated with Segment.ASCAT()..
refGene.table	A table containing gene symbols. If NULL and genome set to "hg18", "hg19" or "hg38", a default list will be used.
targets.table	A table containing a selected list of gene symbols (typically, a list of drug-actionable genes). If NULL and genome set to "hg19", a default list of 475 cancer genes will be used.
report	Generate the HTML report.
author.name	Name of the author/lab/facility to display in the HTML report.
out.dir	The output directory.

Author(s)

Bastien Job

gustaveroussy/EaCoN documentation built on Oct. 20, 2021, 2:41 a.m.