eztoptab: Wrapper for limma topTable function

In jdreyf/ezlimma: Streamlines and extends limma package

Wrapper for limma topTable function

Description

Wrapper for limma topTable function that subsets and changes colnames

Usage

eztoptab(
  fit,
  cols = c("P.Value", "adj.P.Val", "logFC"),
  adjust.method = "BH",
  prefix = NULL,
  coef = NULL
)

Arguments

fit	Object of class MArrayLM as produced by lmFit then eBayes.
cols	Columns of topTable output to include. Possibilities include "logFC", "SE", "AveExpr", "z", "t", "P.Value", "adj.P.Val", "CI.L", "CI.R", "B". Some of these column names are then changed here. If logFC is specified, FC will automatically also be given.
adjust.method	Method used to adjust the p-values for multiple testing. Options, in increasing conservatism, include "none", "BH", "BY", and "holm". See p.adjust for the complete list of options. A NULL value will result in the default adjustment method, which is "BH".
prefix	Character string to add to beginning of column names. NULL does not add a prefix.
coef	Column index or column name specifying which coefficient or contrast of the linear model to test. If length(coef)>1, an F-test will be performed, and logFC & FC will not be returned.

Details

If length(coef)>=2, "z" will not be returned.

Value

Data frame.

See Also

topTable.

jdreyf/ezlimma documentation built on Sept. 16, 2024, 2:08 a.m.