Usage
generate_report(cmap.result, reference, reference.name, annotation.db, element, query, tmp_filename, title = "", max.results = getOption("max.results", default = 50), min.found = getOption("min.found", default = 1), max.padj = getOption("max.padj", default = 0.1), gene.level.report = getOption("gene.level.report", default = TRUE), gene.level.plot = getOption("gene.level.plot", default = TRUE), reportDirectory = tempdir(), excluded.cols = getOption("excluded.cols", default = c("geneScores", "signed", "pval", "UID", "z.shift", "log_fc.shift", "mod_fc.shift")), swap.colnames = getOption("swap.colnames", default = list(padj = "FDR", nFound = "Genes")))
Arguments
cmap.result
CMAPResults object
reference
eSet object, the full reference database, typically an NChannelSet or CMAPCollection object
reference.name
character, the name of the reference database
annotation.db
character, the name of the annotation package used to lookup gene identifiers
element
character, the assayDataElementName to extract from NChannelSet objects
query
a GeneSet, SignedGeneSet or ExpressionSet object used as query for the gene-set-enrichment analysis giving rise to 'cmap.result'
tmp_filename
character, the name of the temporary output folder
title
character, title of the report
max.results
integer, maximum number of results to return
min.found
integer, minimum number of gene set members that need to overlap with the user query. Gene sets with matching members less than min.found will not be returned as results.
max.padj
numeric, maximum adjusted p-value for a gene set to be considered significantly similar. Results with adjusted p-values larger than max.padj will not be returned.
gene.level.report
logical, create gene-level reports ?
gene.level.plot
logical, create gene-level plots ?
reportDirectory
character, path to temporary output directory for this session. Default=tempdir()
excluded.cols
character vector listing columns in the CMAPResults objects that should NOT be included in the report
swap.colnames
list, containing alternative names for CMAPResults columns.