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

Description Usage Arguments Details Value Author(s)

This function reveives the results of a gene-set enrichment analysis and the original reference databases to generate plots and html code elements for the final report.

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")))

`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.

This function is called by the cmapAnalysis function

a list of character strings, either containing html code snippets or paths to result files. These elements are used to brew the final result html page.

Thomas Sandmann

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