RTCGA survival package Breast cancer subtypes
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giulia_m ▴ 10
@giulia_m-16220
Last seen 6.5 years ago

Hello everyone!

 

I used the RTCGA package for survival analyis in different types of cancers from TCGA. I stratified the patients based on high or low expression of two genes. By using the code generated by MarcinKosinski I obtained nice survival curves (https://github.com/RTCGA/RTCGA/issues/97#categorize-variables). The R code he suggests is immediate and very useful!

Now I would like to stratify the patients based on the different breast cancer subtypes (Luminal A, Luminal B etc....) to see if the genes I considered affect the survival of particular subtypes. 

Do you have any suggestions for this? 

How to get clinical and RNA data from each subtype?

 

Best, 

 

Giulia

 

rtcga • 1.8k views
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Hello @giulia_m , can you provide the code, so we can update it with your request?

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Here is the code I used: 

library(RTCGA.clinical)
library(RTCGA.rnaseq)
library(tidyverse)
library(survmnier)

survivalTCGA(BRCA.clinical) -> BRCA.surv
expressionsTCGA(
   BRCA.rnaseq,
   extract.cols = c("CDCA2|157313", "AURKB|9212")
) -> BRCA.rnaseq

dim(BRCA.surv); dim(BRCA.rnaseq)

head(BRCA.surv); head(BRCA.rnaseq)

BRCA.rnaseq <- BRCA.rnaseq %>%
   rename(cohort = dataset,
          CDCA2 = `CDCA2|157313`,
          AURKB = `AURKB|9212`) %>%
   filter(substr(bcr_patient_barcode, 14, 15) == "01") %>% 
   mutate(bcr_patient_barcode = substr(bcr_patient_barcode, 1, 12))

head(BRCA.rnaseq)

BRCA.surv %>%
   left_join(BRCA.rnaseq,
             by = "bcr_patient_barcode") ->
   BRCA.surv_rnaseq

head(BRCA.surv_rnaseq)

table(BRCA.surv_rnaseq$cohort, useNA = "always")

BRCA.surv_rnaseq <- BRCA.surv_rnaseq %>%
   filter(!is.na(cohort))

dim(BRCA.surv_rnaseq)

 

BRCA.surv_rnaseq.cut <- surv_cutpoint(
   BRCA.surv_rnaseq,
   time = "times",
   event = "patient.vital_status",
   variables = c("CDCA2", "AURKB")
)
summary(BRCA.surv_rnaseq.cut)

BRCA.surv %>%
   left_join(BRCA.rnaseq,
             by = "bcr_patient_barcode") ->
   BRCA.surv_rnaseq

head(BRCA.surv_rnaseq)


BRCA.surv_rnaseq.cat <- surv_categorize(BRCA.surv_rnaseq.cut)
headBRCA.surv_rnaseq.cat)

BRCA.surv_rnaseq.cat <- BRCA.surv_rnaseq.cat %>%
   mutate(cohort = BRCA.surv_rnaseq$cohort)
headBRCA.surv_rnaseq.cat)


library(survival)
fit <- survfit(Surv(times, patient.vital_status) ~ CDCA2 + AURKB, 
               data = BRCA.surv_rnaseq.cat)

Thanks!

 

 

 

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@giulia_m is any column name meaningful if you run colnames(BRCA.clinical) then you can specify extract.cols in survivalTCGA . You can try using 


lapply(BRCA.clinical, function(x) {any(grepl('lum', tolower(x)))}) -&gt; is_there_luminal

which(unlist(is_there_luminal))

do detect whether any variables has lum in any name of considered factor levels

table(BRCA.clinical$patient.breast_carcinoma_primary_surgical_procedure_name)
                 lumpectomy              mastectomy nos modified radical mastectomy                       other 
                          9                          18                          14                          14

however I can't find luminal

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Thank you Marcin!

Yes I tried...

I cannot find any indication with "subtypes"...

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I could only check via: http://tumorsurvival.org/TCGA/Breast_TCGA_BRCA/index.html

Here you can select Luminal A, Luminal B etc. 

For example here are the results: http://tumorsurvival.org/TCGA/Breast_TCGA_BRCA/process.php

It is possible to download the excel file but then how should I deal with?

 

 

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Is there a way to download sub-type dependency with the bcr_patient_barcode ? If yes, then one can join this to BRCA.clinical with dplyr::left_join

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