CGDS-R Package not working?
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Entering edit mode
22 months ago
1769mkc ★ 1.2k

This code is from this paper

entrez <-  unique(AnnotationDbi::select(hgu133plus2.db, keys = keys(hgu133plus2.db), columns = c("ENTREZID"))$ENTREZID)

mycgds <-  CGDS("http://www.cbioportal.org/public-portal/")
tcgaAML <- getCancerStudies(mycgds)[1,1]
cases <- getCaseLists(mycgds,tcgaAML)[8,1]
g <-  lapply(split(as.numeric(entrez), seq_along(entrez)%/%500), function(genes) getProfileData(mycgds,genes,getGeneticProfiles(mycgds,tcgaAML)[2,1],cases)) ## load in batches of 500
g <- do.call("cbind", g)

The error

g <-  lapply(split(as.numeric(entrez), seq_along(entrez)%/%500), function(genes) getProfileData(mycgds,genes,getGeneticProfiles(mycgds,tcgaAML)[2,1],cases)) ## load in batches of 500
 Error in `[.data.frame`(df, , 2) : undefined columns selected 
TCGA • 400 views
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