export.gsea.rnk.topTable: Export a limma topTable to a GSEA pre-ranked list. The 'rnk'...

In drmjc/metaGSEA: Meta-analysis of GSEA analyses, including intra- and inter-experiment comparisons

Description

GSEA's Max_probe algorithm
GSEA has 2 modes for collapsing probes to genes: “Max_probe” and “Median_probe”, both work well when the input data is a GCT file, consisting of expression levels. However, I feel pretty strongly that GSEApreRanked needs a 3rd option which chooses the best probe, based on the one that obtained the largest t-statistic in either direction, a “Best_probe” if you will. If you provide this function a probe2gene map (from probe ids to gene symbols), then we will automatically export just the best probes, ie 1 row per gene, still using the probe ID as the identifier (so that we can still use the same chip file).

Usage

export.gsea.rnk.topTable(tt, file, values = c("t", "logFC", "P.Value"),
  probe2gene = NULL, convert2symbol = FALSE, verbose = TRUE)

Arguments

tt	a limma topTable
file	the output file <****.rnk>
values	choose the column name that contains the values. This must be in the colnames of the topTable. If P.Value is chosen, then the -log10 P will be calculated, thus small P-values become large +ve numbers. Default is “t”.
probe2gene	a 2 column matrix-like object with mappings from probes 2 genes. Preferably, this will be the chip file used for the GSEA. This allows the identification of the best performing probe per gene, rather than GSEA's "Max_Probe" method which chooses the probe with the larges value which is unsuitable for down-regulated genes where one poorly performing probe could be ~0. Leave as NULL to ignore this.
convert2symbol	logical: if probe2gene!=NULL, then after collapsing to the best probe-per-gene, export the genesymbol (TRUE), or the probe ID (FALSE)?
verbose	logical: verbose messages

Details

probe2gene
The justification for probe2gene is described above. probe2gene should be a 2 column matrix-like object with mappings from probes 2 genes. Preferably, this will be from the same chip file that will be used for running GSEA.

Author(s)

Mark Cowley, 8/2/08

See Also

topTable

drmjc/metaGSEA documentation built on Aug. 8, 2020, 1:53 p.m.