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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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Where could find geneInfo #19

Closed huwenhuo closed 8 years ago

huwenhuo commented 8 years ago

For example here: dataNorm <- TCGAanalyze_Normalization(tabDF = dataBRCA, geneInfo = geneInfo)

I just cann't where is the geneInfo come from. Thanks.

tiagochst commented 8 years ago

The information is in TCGAbiolinks::geneInfo @torongs82 Could you give the source?

torongs82 commented 8 years ago

Hi @huwenhuo thank you writing and @tiagochst pointing out. We created geneInfo to use with TCGAanalyze_Normalization and allowing user to normalize mRNA transcripts and miRNA, using EDASeq package. You can take a look in our vignette. In particular you can run this example to update it:

require(biomaRt) require(EDASeq) data <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") ensemblids <- getBM(attributes=c("ensembl_gene_id"), mart=data) dataGene <- getGeneLengthAndGCContent(id=ensemblids$ensembl_gene_id[1:5], org="hsa")

Best, Antonio.

ghost commented 6 years ago

hi, What to use in geneInfo for miRNAs ? Thanks @tiagochst