Question: retrieving survival informations from cBioportal using Rstudio
1
gravatar for ghadou.ouss
11 months 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 • 340 views
ADD COMMENTlink modified 11 months ago by Biostar ♦♦ 20 • written 11 months 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 11 months ago by Kevin Blighe59k

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 11 months ago by genomax83k • written 11 months 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 11 months ago • written 11 months ago by genomax83k

thank you Mr.genomax for your advice

ADD REPLYlink written 11 months 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 11 months ago • written 11 months ago by Kevin Blighe59k
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