import.gsea.topTable: Import the tabular results from a GSEA PreRanked run

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

Description

Import the tabular results from a GSEA PreRanked run - ie the GSEA top table.

Usage

import.gsea.topTable(dir, sort.by = c("NES", "absNES", "FDR", "P", "SIZE"))

Arguments

dir	the dir that contains the index.html
sort.by	which column to sort by.
NES	decreasing NES score
absNES	decreasing absolute NES score
FDR	increasing FDR, breaking ties by largest absolute NES
P	increasing nomimal P value, breaking ties by largest absolute NES
SIZE	decreasing gene set size

Details

Takes the pos and neg results, and merges them into a single table, adding a DIRECTION column. Then re-sort the rows by NES (default), absolute NES, FDR, P or SIZE (largest->smallest)

Value

a single data.frame with all genesets from within a collection. Unlike the raw GSEA output, this contains a DIRECTION column (up/down) and a LEADING.EDGE.SIZE column which is the number of genes in the leading edge +/- 1 due to rounding errors (this data comes from the tags field in the LEADING.EDGE column), and a RANK.IN.REPORT column which shows the rank in the original list

Author(s)

Mark Cowley, 2009-04-28

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