[BioC] genefilter displaying the expression set

[Martin Morgan]

Hi Dhaarini -- 
dhaarini s <dhaarini87 at gmail.com> writes:

> Hi all!
> I am new to R and Bioconductor. I am having a dataset of 22283 genes and 190
> samples. Due to the huge size of the data, I want to filter some irrelevant
> genes. I tried the "genefilter" package of BioC, but then understand that it
> does gene filtering by simply displaying whether the gene satifies the
> filter condition or not by marking it as TRUE. This is how I proceeded:
>> library(genefilter)
>> f1 <- kOverA(5, 10)
>> flist <- filterfun(f1)
>> ans <- genefilter(tumor, flist)
> (The object "tumor" contains my expression dataset.) The output is something
> like this:
> "x"
> "1007_s_at" TRUE
> "1053_at" FALSE
> "117_at" FALSE
> "121_at" FALSE
> "200001_at" TRUE
> "200002_at" TRUE

just use the logical vector returned by genefilter to subset tumor, e.g.,

filteredTumor <- turmor[genefilter(turmor, flist),]

You can think of 'tumor' as a matrix, with rows being features and
columns samples. You're selecting the rows of 'tumor' that satisfy the
filter criteria.

Martin

> But, Iwould like to know whether the genefilter will return me an expression
> set containing the filtered genes and their expression values for the
> samples. Please help me out!
> Thanks in advance.
> Regards,
> Dhaarini
>
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>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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