Open Vanhesling opened 7 years ago
I have the same problem
Have you solved the problem?
same here, did you find any solution?
TabCoxNet <- TCGAvisualize_SurvivalCoxNET(dataClin, dataFilt, Genelist = rownames(dataSurv), scoreConfidence = 700, org.Hs.string = org.Hs.string, titlePlot = "coad") Error in
[.data.frame
(x, r, vars, drop = drop) : undefined columns selected !
nope
朱奕彰(ZhuYiZhang, Van Helsing) 北京大学医学部基础医学院基础医学 Peking University Health Science Center
北京大学国家发展研究院CCER经济学 NationalSchool of Development, Peking University CCER Tel: 86-18910549981 On 08/09/2018 08:48, RahelSh wrote:
same here, did you find any solution?
TabCoxNet <- TCGAvisualize_SurvivalCoxNET(dataClin,
dataFilt,
Genelist = rownames(dataSurv),
scoreConfidence = 700,
org.Hs.string = org.Hs.string,
titlePlot = "coad")
Error in [.data.frame(x, r, vars, drop = drop) : undefined columns selected !
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.
Any Solution?
Hi Guys I thing that I recognize where the problem is. I have got it as well during analysis of HNSC tumors. I check TCGAvisualize_SurvivalCoxNET function. In the code there is: cfu <- as.data.frame(subset(cfu, select = c("bcr_patient_barcode", "days_to_last_followup", "days_to_death", "vital_status", "age_at_initial_pathologic_diagnosis", "gender"))) but I have slightly different column names of dataClin that course error :undefined columns selected I had:names(dataClin)[24] [1] "days_to_last_follow_up" #(instead of "days_to_last_followup" and names(dataClin)[8] [1] "age_at_diagnosis" # insited of "age_at_initial_pathologic_diagnosis" so solution in my dataClin was: names(dataClin)[24]<-"days_to_last_followup" names(dataClin)[8]<-"age_at_initial_pathologic_diagnosis" After changing the names everything work correctly. I hope that I help in dealing with this problem
Thank u so much!
朱奕彰(ZhuYiZhang, Van Helsing) 北京大学医学部基础医学院基础医学 Peking University Health Science Center
北京大学国家发展研究院CCER经济学 NationalSchool of Development, Peking University CCER Tel: 86-18910549981 On 07/29/2019 18:49, MarcinRuc wrote:
Hi Guys I thing that I recognize wher e the problem is. I have got it as well during analysis of HNSC tumors. I check TCGAvisualize_SurvivalCoxNET function. In the code there is: cfu <- as.data.frame(subset(cfu, select = c("bcr_patient_barcode", "days_to_last_followup", "days_to_death", "vital_status", "age_at_initial_pathologic_diagnosis", "gender"))) but I have slightly different column names of dataClin that course error :undefined columns selected I had:names(dataClin)[24] [1] "days_to_last_follow_up" #(instead of "days_to_last_followup" and names(dataClin)[8] [1] "age_at_diagnosis" # sited of age_at_initial_pathologic_diagnosis so solution in my dataClin was: names(dataClin)[24]<-"days_to_last_followup" names(dataClin)[8]<-"age_at_initial_pathologic_diagnosis" After changing the names everything work correctly. I hope that I help in dealing wit this problem
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or mute the thread.
No problem I glad that I was able to help
Hi Guys I thing that I recognize where the problem is. I have got it as well during analysis of HNSC tumors. I check TCGAvisualize_SurvivalCoxNET function. In the code there is: cfu <- as.data.frame(subset(cfu, select = c("bcr_patient_barcode", "days_to_last_followup", "days_to_death", "vital_status", "age_at_initial_pathologic_diagnosis", "gender"))) but I have slightly different column names of dataClin that course error :undefined columns selected I had:names(dataClin)[24] [1] "days_to_last_follow_up" #(instead of "days_to_last_followup" and names(dataClin)[8] [1] "age_at_diagnosis" # insited of "age_at_initial_pathologic_diagnosis" so solution in my dataClin was: names(dataClin)[24]<-"days_to_last_followup" names(dataClin)[8]<-"age_at_initial_pathologic_diagnosis" After changing the names everything work correctly. I hope that I help in dealing with this problem
Your reply has exactly solved my problem. Thank you very much!
Hi Guys I thing that I recognize where the problem is. I have got it as well during analysis of HNSC tumors. I check TCGAvisualize_SurvivalCoxNET function. In the code there is: cfu <- as.data.frame(subset(cfu, select = c("bcr_patient_barcode", "days_to_last_followup", "days_to_death", "vital_status", "age_at_initial_pathologic_diagnosis", "gender"))) but I have slightly different column names of dataClin that course error :undefined columns selected I had:names(dataClin)[24] [1] "days_to_last_follow_up" #(instead of "days_to_last_followup" and names(dataClin)[8] [1] "age_at_diagnosis" # insited of "age_at_initial_pathologic_diagnosis" so solution in my dataClin was: names(dataClin)[24]<-"days_to_last_followup" names(dataClin)[8]<-"age_at_initial_pathologic_diagnosis" After changing the names everything work correctly. I hope that I help in dealing with this problem
This solved my problem! I did change the code to fix the problem slightly. It seems that the index for the "days_to_last_follow_up" and "age_at_diagnosis" are variable so a generic fix is: colnames(dataClin)[which(names(dataClin) == "days_to_last_follow_up")] <- "days_to_last_followup" colnames(dataClin)[which(names(dataClin) == "age_at_diagnosis")] <- "age_at_initial_pathologic_diagnosis"
Hi,
When I executed the code of vignette (Part: Case study n. 1 - Pan Cancer downstream analysis BRCA), however, I can’t get the TabCoxNet plot by using the TCGAanalyze_SurvivalCoxNET function. It seems that this error is same with issue #32 reported. So I was wondering if there are any bugs in the TCGAanalyze_SurvivalCoxNET function or how could I fix this issue and get the correct plot?
Thanks, Kevin