export.gsea.odf.lmFit: Export a limma lmFit to a GSEA ODF file. From two linear...

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

Description

This is a key function for the LimmaGP GenePattern module. In LimmaGP, we always perform two linear model fits, the first is a treatment means parameterisation (fit1, hereafter), the second is a contrast fit after constructing the appropriate contrasts (fit2, hereafter). From fit1, we can get the group means, and standard errors, and from fit2, we can get the logFC, moderated t-statistics, pvalues, and FDR/FWER values.

Usage

export.gsea.odf.lmFit(fit1, fit2, coef = 1, file, gct.file, cls.file,
  description, collapse = FALSE, probe2gene = NULL)

Arguments

fit1	a linear model fit, before fitting contrasts, and running eBayes
fit2	a linear model fit, after fitting contrasts, and running eBayes
coef	the coefficient to be exported. see topTable
file	the path to the ODF file
gct.file	the name of the gct file that the linear models were fitted to. This is written to the ODF header
cls.file	the name of the cls file that the linear models were fitted to. This is written to the ODF header
description	a character vector, which will end up in the description column. if NULL, then the probe ID's will be used.
collapse	logical: whether to collapse probes to genes? if TRUE, then probe2gene must be set.
probe2gene	if collapse=TRUE, then a 2 column data.frame mapping from probe to gene symbol should be supplied. default: NULL.

Value

nothing. writes an ODF file.

Author(s)

Mark Cowley, 2011-07-19

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