Filter CNVs if contain certain gene
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julrodr80 ▴ 30
@julrodr80-11991
Last seen 3.9 years ago

I have a GR objetc, a list of cnvs with its genes; its possible to subset this cnvs if they have al least one gene of a list of genes?

cnv genomic ranges cnvs • 515 views
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Probably, but you will have to be more descriptive than that. Do you have one GRanges object with genes in the mcols, or a GRanges object and a list of genes?

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In the same line as  James W. MacDonald.

You probably can get more help if you could show us a few lines of your GRanges object.

If gene names are stored as names of ranges:

    idx = which(names(gr) %in% gene.list)

    gr = gr[idx, ]

If gene names are stored as a column in elementMetadata slot:

    idx = which(mcols(gr)[ ,"Gene_Symbol"] %in% gene.list)

    gr = gr[idx, ]

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