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Function for removing low expressed genes

Dear All,

I have a matrix contains the gene names at the first columns and the rest of columns in this matrix represent the gene expression in different tissues. My question is how to write a function or line in R to remove the rows that have expression less than specific value say 5.

r
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updated by Ram Ram • written by M K M K

3 answers

If you want to remove all the rows that never have expression of 5 or higher:

matrix[apply(matrix[,-1],1,function(X) length(X[X>=5])>0 ),]
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written by 5utr 5utr

Thanks Gian.

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written by M K M K

If this answers your question please accept the answer

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written by 5utr 5utr

edgeR approach filters by counts per million (CPM), see for example page 11 of the user guide. y is a DGEList:

keep <- rowSums(cpm(y)>1) >= 2
y <- y[keep, , keep.lib.sizes=FALSE]
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written by h.mon h.mon

Have a look at the genefilter package in Bioconductor. In particular, note the kOverA() function.

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updated by Ram Ram • written by Devon Ryan Devon Ryan

I just need simple R line because I am using this file for testing something else (i.e easy line to do this regardless the first column if it is gene name oe anything else)

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written by M K M K

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