export.gsea.rnk: Export a vector of values as a GSEA pre-ranked list.

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

Description

Export a vector of values as a GSEA pre-ranked list.

Usage

export.gsea.rnk(values, names = NULL, file = NULL, resort = TRUE,
  sigfigs = 4, up.class = NA, down.class = NA)

Arguments

values	a numeric vector
names	the names associated with each value. If NULL, then the names(values) are used
file	the output file name. No hyphens, or a warning will be issued.
resort	logical: re-sort the values such that they are decreasing? see order(, decreasing=TRUE)
sigfigs	the number of significant figures, defaults to 4.
up.class	The up-regulated genes are up in up.class
down.class	The down-regulated genes are down in down.class

Details

Specifying up-/down-regulated genes. One of the biggest causes of confusion, especially when revisiting results generated a long time ago, are my positive genes up in class A, or class B? If you specify up.class and down.class, a header is written into in the rnk file. The new GseaPreRanked GenePattern module will read that header & label the geneset reports with these names, rather than na_pos and na_neg.

Value

<none>, makes a file

Author(s)

Mark Cowley, 2008-09-08

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