enrichDF2enrichResult: Convert data.frame to enrichResult

In jmw86069/jamenrich: Analysis and Visualization of Multiple Gene Set Enrichments

Convert data.frame to enrichResult

Description

Convert data.frame to enrichResult

Usage

enrichDF2enrichResult(
  enrichDF = NULL,
  pvalueCutoff = 1,
  pAdjustMethod = "none",
  keyColname = c("itemsetID", "ID", "Name", "Pathway"),
  pathGenes = "pathGenes",
  geneColname = c("geneNames", "geneID", "Gene", "Genes"),
  geneHits = "geneHits",
  geneRatioColname = c("GeneRatio", "^Ratio"),
  geneDelim = "[,/ ]+",
  geneSep = ",",
  pvalueColname = c("P.Value", "Pvalue", "FDR", "adj.P.Val"),
  descriptionColname = c("Description", "Name", "Pathway", "ID"),
  msigdbGmtT = NULL,
  verbose = FALSE,
  ...
)

Arguments

enrichDF	data.frame representing gene set enrichment results.
pvalueCutoff	numeric value range 0 to 1, to define the P-value threshold for enrichment results to be considered in downstream processing.
pAdjustMethod	character string to define the P-value adjustment method, or "none" for no additional adjustment. See stats::p.adjust() for valid values.
keyColname	character value of the colname(enrichDF) containing the unique row identifier. It can be a pathway_ID or any uniquely identifying value.
pathGenes	character or value of the colname(enrichDF) containing the number of genes in each pathway. This value will be derived from geneRatioColname if needed.
geneColname	character value of the colname(enrichDF) containing delimiited genes in each pathway.
geneHits	character value of the colname(enrichDF) containing the integer count of the gene hits in each pathway. This value will be derived from geneRatioColname if needed.
geneRatioColname	character value of the colname(enrichDF) containing the character ratio of gene hits to pathway size, in format "50/100". This value is used when either "pathGenes" or "geneHits" are not supplied.
geneDelim	character regular expression pattern used to separate genes in the pathGenes column into a vector of character values.
pvalueColname	character value of the colname(enrichDF) containing enrichment P-values to use in downstream processing.
msigdbGmtT	optional gmtT object, a representation of arules::transactions-class. (Not currently implemented.)
verbose	logical indicating whether to print verbose output.
...	additional arguments are ignored.

Details

This function takes a data.frame containing gene set enrichment results, and converts it to a proper enrichResult object, compatible with methods provided by the clusterProfiler package.

See Also

Other jam conversion functions: cnet2df(), cnet2im(), enrichList2IM(), enrichList2df(), enrichMapJam()

jmw86069/jamenrich documentation built on Feb. 3, 2024, 12:40 p.m.