Question: I am trying to get the promoters of a set of differentially expressed genes
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gravatar for Fawzi Yassine
4 months ago by
Fawzi Yassine10 wrote:

I am trying to get the promoters of a set of differentially expressed genes (diff.expressed.genes.id)

dimdiff.expressed.genes.id)[1]

13003

txdb = TxDb.Hsapiens.UCSC.hg19.knownGene

txdb.genes = genes(txdb)

length(txdb.genes)

23056

diff.expressed.gene.promoters = promoters(txdb.genes[txdb.genes$gene_id %in% diff.expressed.genes.id$ENTREZID])

length(diff.expressed.gene.promoters)

7892.

In fact

table(txdb.genes$gene_id %in% diff.expressed.genes.id$ENTREZID)["TRUE"]

  1. What's wrong?

I was expecting (hoping) that length(diff.expressed.gene.promoters) is dimdiff.expressed.genes.id)[1]

13003 same as dimdiff.expressed.genes.id)[1]

thanks,

rna-seq chip-seq • 172 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by Fawzi Yassine10
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