plot_gsea.leadingedge.HCL.auto: Automated GSEA HCL

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

Description

Automated method for doing a hierarchical clustering of genesets, based on each sets leading edge genes, for all gsea results in a list of gsea results, over a range of different best N, FDR, P, FWER thresholds, and for up/down genesets.

Usage

plot_gsea.leadingedge.HCL.auto(x, file = NULL, N = c(50), FDR = c(0.25),
  P = NULL, FWER = NULL, max.distance = 1)

Arguments

x	either a gsea list, or a list of gsea lists. see import.gsea
file	either the path to a pdf file which will be created, or NULL to use the current plotting device
N	vectors of 0 or more thresholds to use. eg N=c(50, 100) means plot the top 50, or the
FDR	vectors of 0 or more thresholds to use. eg N=c(50, 100) means plot the top 50, or the
P	vectors of 0 or more thresholds to use. eg N=c(50, 100) means plot the top 50, or the
FWER	vectors of 0 or more thresholds to use. eg N=c(50, 100) means plot the top 50, or the top 100 genesets
max.distance	(experimental) threshold to filter out genesets that are poorly connected to each other. This is a distance threshold, so 1.0 means all genesets, 0.9 is a good place to start.

Value

makes a number of plots to a pdf file, or the current plotting device

Author(s)

Mark Cowley, 2009-09-03

See Also

plot_gsea.leadingedge.HCL, gsea.leadingedge.distance

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