Question: FirebrowseR retrive all the genes expression
1
gravatar for rbrtdambrosio
3.9 years ago by
rbrtdambrosio70 wrote:

Hello,

I'm trying to collect the data from the TCGA COAD project using FirebrowseR. I'm fallowing the "how to use" manual https://github.com/mariodeng/FirebrowseR/blob/master/vignettes/FirebrowseR.Rmd

I would like to modify the following section in order to retrive all the genes expression values for each sample. Unfortunately the function Samples.mRNASeq require a list of gene names. There is a way to retrive all the expression values without specify the single names? Eventually were I could take the full gene list ?

  diff.Exp.Genes = c("ESR1", "GATA3", "XBP1", "FOXA1", "ERBB2", "GRB7", "EGFR",
                   "FOXC1", "MYC")

all.Found = F 

page.Counter = 1

mRNA.Exp = list()

page.Size = 2000 # using a bigger page size is faster
while(all.Found == F){
  mRNA.Exp[[page.Counter]] = Samples.mRNASeq(format = "csv",
                                             gene = diff.Exp.Genes,
                                             cohort = "BRCA",
                                             tcga_participant_barcode =
                                               brca.Pats$tcga_participant_barcode,
                                             page_size = page.Size,
                                             page = page.Counter)
  if(nrow(mRNA.Exp[[page.Counter]]) < page.Size)
    all.Found = T
  else
    page.Counter = page.Counter + 1
}
mRNA.Exp = do.call(rbind, mRNA.Exp)
dim(mRNA.Exp)

Thanks

rna-seq firebrowser • 2.3k views
ADD COMMENTlink modified 3.9 years ago by Mdeng510 • written 3.9 years ago by rbrtdambrosio70

Can we enter all the 20500 genes in genes argument to get all the expression values??

ADD REPLYlink written 3.4 years ago by shashank.jatav30
1
gravatar for Mdeng
3.9 years ago by
Mdeng510
Germany
Mdeng510 wrote:

Sadly the API is not designed for these purposes. It's likely more intended to provide a light interface for pre-build queries, which e.g. could be included in an application etc..

To bulk download data sets for an entire cohort I would recommend using GDAC or you could still user FirebrowseR using the Archives.StandardData function. Based on its query parameters it will provide you with a list of archives which can be download, so you don't have to narrow down the bulk data yourself.

ADD COMMENTlink written 3.9 years ago by Mdeng510

oh it's a pity. Thanks for the interesting suggestions!

ADD REPLYlink written 3.9 years ago by rbrtdambrosio70
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