tableFilt: Filter a topTable object

In jmacdon/affycoretools: Functions useful for those doing repetitive analyses with Affymetrix GeneChips

Filter a topTable object

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

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 <[e-mail]>

jmacdon/affycoretools documentation built on Feb. 25, 2023, 4:51 a.m.