tableFilt: Filter a topTable object

Description Usage Arguments Value Author(s)

View source: R/reportingTools.R

Description

This function is designed to filter genes from a topTable object based on p-value and/or fold change. This is an internal function and is not intended to be called by thte end user.

Usage

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tableFilt(fit, coef = 1, number = 30, fldfilt = NULL, pfilt = NULL,
  adjust = "fdr")

Arguments

fit

An MArrayLM object, resulting from a call to eBayes

coef

The contrast to be extracted into the topTable. See ?topTable for more information.

number

The number of genes to output. Only used if both foldfilt and pfilt are NULL.

fldfilt

The absolute value of fold difference to filter on. This assumes the data are log transformed.

pfilt

The p-value to filter on.

adjust

The multiplicity adjustment to use. Options are '"bonferroni"', '"holm"', '"hochberg"', '"hommel"', '"fdr"' and '"none"'. If '"none"' then the p-values are not adjusted. A 'NULL' value will result in the default adjustment method, which is '"fdr"'.

Value

Returns a data.frame containing the selected genes.

Author(s)

James W. MacDonald <[email protected]>


affycoretools documentation built on July 29, 2018, 10 a.m.