This function compiles a gene-level report from a CMAPResults object.

Description

Usually called by the generate_report function

Usage

1
2
3
4
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

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.