Question: retrieving survival informations from cBioportal using Rstudio
1
gravatar for ghadou.ouss
5 weeks ago by
ghadou.ouss0 wrote:

Hello dear community, i want to retrieve all the informations about "Glioblastoma" study (Nature 2008) using Rstudio from cBioportal. Selected genes: "COL4A1, PDPN, GDF15, IGFBP2, SPARCL1, SPRY1, VEGFA, RBP1, NRP2, MFF ,TSPAN6, SGCD ,FZD7, HBA2, HBA1, CAVIN1, MTSS1, DICER1, BASP1, CXCR4, OAS1, NDP, CCN1, PTPRZ1, GPNMB, BTG2 ,GATM ,RUFY3, LUM, GBP1, PLCB1, PLP1, SCG2, CSRP2, CRYAB, SGK1, COL4A2, COL11A1, COL6A3, IGFBP3, KYNU ,SERPINE1, CMTM3, DNAJC12, PTHLH, ANXA1, VIM, NAV1, HBEGF, TAGLN, IGF2BP3, CRISPLD2, COL13A1, LDB3"

Can somebody lead me. help would be so appreciated.

survival rna-seq R gene • 212 views
ADD COMMENTlink modified 5 weeks ago by Biostar ♦♦ 20 • written 5 weeks ago by ghadou.ouss0
1

What have you already tried to do? Do you not know where the survival information can be found? Did you look at the functions on the cBioPortal website already (rudimentary survival analysis is possible via the website)?

ADD REPLYlink written 5 weeks ago by Kevin Blighe45k

Thank you for your response Mr. Kevin, actually i used the 'cgsdr' package related to cBioportal, here is my code on Rstudio:

install.packages('cgdsr')
library(R.utils)
library(cgdsr)
# Create CGDS object
mycgds = CGDS("https://www.cbioportal.org/")
# Test the CGDS endpoint URL using a few simple API tests
test(mycgds)
# retrieving glioblastoma informations
mygeneticprofil = getGeneticProfiles(mycgds,'gbm_tcga_pub')[,c(1:2)]
mycancerstudy = getCancerStudies(mycgds, 'gbm_tcga_pub')[81,1]
mycaselist = getCaseLists(mycgds,mycancerstudy)[1,1]
mygeneticprofile = getGeneticProfiles(mycgds,mycancerstudy)[4,1]
getProfileData(mycgds,c('PTEN','ERBB2'),mygeneticprofile,mycaselist)
gbm_tcga_mutations = getMutationData(mycgds,mycaselist,mygeneticprofile,c('ERBB2','PTEN')) # just for 2 genes

But for me it seems to be not clear visualizing it on the screen of console. i want to do something like: getting survival results as CSV format or plot.

ADD REPLYlink modified 5 weeks ago by genomax69k • written 5 weeks ago by ghadou.ouss0

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by genomax69k

thank you Mr.genomax for your advice

ADD REPLYlink written 5 weeks ago by ghadou.ouss0

If I run your code, I receive an error message:

getProfileData(mycgds,c('PTEN','ERBB2'),mygeneticprofile,mycaselist)
[1] Error..Problem.when.identifying.a.cancer.study.for.the.request.

Also, why do you have these 2 lines of code?

mygeneticprofil = getGeneticProfiles(mycgds,'gbm_tcga_pub')[,c(1:2)]
...
mygeneticprofile = getGeneticProfiles(mycgds,mycancerstudy)[4,1]

Sorry, can you please contact cBioPortal directly for help?

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Kevin Blighe45k
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