geneFilter: filter an ExpressionSet using different methods

Description Usage Arguments Details Value Author(s) Examples

View source: R/geneFilter.R

Description

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

Usage

1
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

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2

ArrayTools documentation built on May 2, 2018, 3:04 a.m.