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

Description Usage Arguments Value Author(s)

View source: R/export.gsea.odf.lmFit.R

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

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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.