geneFilter: filter an ExpressionSet using different methods

In ArrayTools: geneChip Analysis Package

Description

Create a filtered 'ExpressionSet' based on background, range, or interquartile range

Usage

geneFilter(object, pct = 0.1, numChip = ceiling(ncol(exprs(object)) * pct), bg = 4, range = 0, iqrPct = 0, output = FALSE, mydir = getwd())

Arguments

object	an ExpressionSet
pct	percentage
numChip	number of chips. If you would like to filter the ExpressionSet based on at least 3 chips greater than 1 (bg=1), then set numChip = 3
bg	background value. If you would like to filter the ExpressionSet based on at least 3 chips greater than 1, then set bg=1
range	range = max value - min value of each gene
iqrPct	interquartile percentage
output	if output = TRUE, output filtered data in the sepecified directory
mydir	the directory containing the filtered data

Details

There are three filtering methods. The User can use either one, two, or three. 1). At least a certain number of chips (numChip) are greater than a given background (bg) 2). The range of the gene have to be greater than a given value (range) 3). Calulating the interquatile range (IQR) of each gene to create an IQR vector. Based on the given percentage (e.g. iqrPct=0.2), find the corresponding percentile. If IQR is less than percentile, the gene will be filtered

Value

a filtered ExpressionSet

Author(s)

Xiwei Wu, Arthur Li

Examples

data(eSetExample)
filtered <- geneFilter(eSetExample)

ArrayTools documentation built on Nov. 8, 2020, 8:13 p.m.