TCGAnalyze_SurvivalCoxNET function

[Vanhesling]

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

> dataSurv <- TCGAanalyze_SurvivalKM(clinical_patient = dataClin,
+                                    dataGE = dataFilt,
+                                    Genelist = rownames(dataDEGs),
+                                    Survresult = FALSE,
+                                    ThreshTop = 0.67,
+                                    ThreshDown = 0.33,
+                                    p.cut = 0.05, group1, group2)
3539.3538.3537.3536.3535.3534.3533.3532.3531.3530.3529.3528.3527.3526.3525.3524.3523.3522.3521.3520.3519.3518.3517.3516.3515.3514.3513.3512.3511.3510.3509.3508.3507.3506.3505.3504.3503.3502.3501.3500.3499.3498.3497.3496.3495.3494.3493.3492.3491.3490.3489.3488.3487.3486.3485.3484.3483.3482.3481.3480.3479.3478.3477.3476.3475.3474.3473.3472.3471.3470.3469.3468.3467.3466.3465.3464.3463.3462.3461.3460.3459.3458.3457.3456.3455.3454.3453.3452.3451.3450.3449.3448.3447.3446.3445.3444.3443.3442.3441.3440.3439.3438.3437.3436.3435.3434.3433.3432.3431.3430.3429.3428.3427.3426.3425.3424.3423.3422.3421.3420.3419.3418.3417.3416.3415.3414.3413.3412.3411.3410.3409.3408.3407.3406.3405.3404.3403.3402.3401.3400.3399.3398.3397.3396.3395.3394.3393.3392.3391.3390.3389.3388.3387.3386.3385.3384.3383.3382.3381.3380.3379.3378.3377.3376.3375.3374.3373.3372.3371.3370.3369.3368.3367.3366.3365.3364.3363.3362.3361.3360.3359.3358.3357.3356.3355.3354.3353.3352.3351.3350.3349.3348.3347.3346.3345.3344.3343.3342.3341.3340.... <truncated>
> TabCoxNet <- TCGAvisualize_SurvivalCoxNET(dataClin,
+                                           dataFilt, 
+                                           Genelist = rownames(dataSurv),
+                                           scoreConfidence = 700,
+                                           org.Hs.string = org.Hs.string,
+                                           titlePlot = "Case Study n.1 dnet")
Error in `[.data.frame`(x, r, vars, drop = drop) : 
  undefined columns selected

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936  LC_CTYPE=Chinese (Simplified)_China.936   
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C                              
[5] LC_TIME=Chinese (Simplified)_China.936    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] dnet_1.0.10                supraHex_1.12.0            hexbin_1.27.1             
 [4] igraph_1.0.1               TCGAbiolinks_2.5.3         SummarizedExperiment_1.4.0
 [7] Biobase_2.34.0             GenomicRanges_1.26.1       GenomeInfoDb_1.10.3       
[10] IRanges_2.8.1              S4Vectors_0.12.1           BiocGenerics_0.20.0       

[gynecoloji]

I have the same problem

[gynecoloji]

Have you solved the problem?

[Rahel14350]

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 !

[Vanhesling]

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 !

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[SomayahAlbaradei]

Any Solution?

[MarcinRuc]

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

[Vanhesling]

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

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[MarcinRuc]

No problem I glad that I was able to help

[tzjyxb]

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!

[dkeifenheim]

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"