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

Description Usage Arguments Value Author(s)

View source: R/reporting.R

Description

Usually called by the generate_report function

Usage

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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 Nov. 17, 2017, 12:30 p.m.