create_gene_report

cmap.result

a GeneSet, SignedGeneSet or ExpressionSet object used as query for the gene-set-enrichment analysis giving rise to 'cmap.result'

query

character, path to gene_results folder in the per-session output directory

result.dir

character, the name of the reference database

url.base

eSet, the reference database used for the gCMAP analysis

reference.cmap

character, path to figure folder in the per-session output directory

figure.dir

character, the assayDataElementName to extract from NChannelSet objects

element

character, the name of the annotation package used to lookup gene identifiers

annotation.db

logical: should gene-level plots be included in the report ?

gene.level.plot,


Usually called by the generate_report function


The gCMAPWeb R package provides a graphical user interface
for the gCMAP package. gCMAPWeb uses the Rook package and can
be used either on a local machine, leveraging R's internal web
server, or run on a dedicated rApache web server installation.
gCMAPWeb allows users to search their own data sources and
instructions to generate reference datasets from public
repositories are included with the package. The package
supports three common types of analyses, specifically queries
with 1. one or two sets of query gene identifiers, whose
members are expected to show changes in gene expression in a
consistent direction. For example, an up-regulated gene set
might contain genes activated by a transcription factor, a
down-regulated geneset targets repressed by the same factor. 2.
a single set of query gene identifiers, whose members are
expected to show divergent differential expression
(non-directional query). For example, members of a particular
signaling pathway, some of which may be up- some down-regulated
in response to a stimulus. 3. a query with the complete results
of a differential expression profiling experiment. For example,
gene identifiers and z-scores from a previous perturbation
experiment. gCMAPWeb accepts three types of identifiers:
EntreIds, gene Symbols and microarray probe ids and can be
configured to work with any species supported by Bioconductor.
For each query submission, significantly similar reference
datasets will be identified and reported in graphical and
tabular form.

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

Description

Usage

Arguments

Value