geneFilter {ArrayTools} | R Documentation |
Create a filtered 'ExpressionSet' based on background, range, or interquartile range
geneFilter(object, pct = 0.1, numChip = ceiling(ncol(exprs(object)) * pct), bg = 4, range = 0, iqrPct = 0, output = FALSE, mydir = getwd())
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 |
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
a filtered ExpressionSet
Xiwei Wu, Arthur Li
data(eSetExample) filtered <- geneFilter(eSetExample)