topTable.all: Run topTable on all contrasts from a linear model fit...
In drmjc/microarrays: A collection of microarray and genomic helper code.

Description Usage Arguments Value Author(s)

Run topTable on all contrasts from a linear model fit Function to create a topTable for every contrast from an lmFit object, including the F-stat, if >1 contrasts

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  topTable.all(fit, number = Inf, genelist = fit$genes,
    adjust.method = "BH", sort.by = "p", resort.by = NULL,
    p.value = 1, lfc = 0)

`fit`	an `lmFit` object
`number`	the number of DE genes. default=Inf which is all genes tested
`genelist`	vector of genes to do the topTable on
`adjust.method`	the multiple test correction method. default=“BH”. see `topTable`
`sort.by`	which column to sort by? see `topTable`
`resort.by`	character string specifying statistic to sort the selected genes by in the output `data.frame`. Possibilities are the same as for `sort.by`.
`p.value`	a p.value threshold. default=1.0, ie all genes
`lfc`	a logFC threhsold to use. default=0.0, ie all genes