create_gene_report: This function compiles a gene-level report from a CMAPResults...

In gCMAPWeb: A web interface for gene-set enrichment analyses

Description

Usually called by the generate_report function

Usage

create_gene_report(cmap.result, query, result.dir, url.base, reference.cmap,
  figure.dir, element = getOption("element", default = "z"),
  annotation.db = "org.Hs.eg.db",
  gene.level.plot = getOption("gene.level.plot", default = TRUE))

Arguments

cmap.result	a CMAPResults object
query	a GeneSet, SignedGeneSet or ExpressionSet object used as query for the gene-set-enrichment analysis giving rise to 'cmap.result'
result.dir	character, path to gene_results folder in the per-session output directory
url.base	character, the name of the reference database
reference.cmap	eSet, the reference database used for the gCMAP analysis
figure.dir	character, path to figure folder in the per-session output directory
element	character, the assayDataElementName to extract from NChannelSet objects
annotation.db	character, the name of the annotation package used to lookup gene identifiers
gene.level.plot,	logical: should gene-level plots be included in the report ?

Value

character string with the relative url to the report html, which is directly written to disk.

Author(s)

Thomas Sandmann

gCMAPWeb documentation built on April 28, 2020, 8:23 p.m.