A problem to manual

[cx-333]

Dear friends, now I want to learn how use the TCGAbiolinks package, but I can not found it in the given website. Could you offer me some relavent data ? Thank you very much !!!

[troysgit]

I think you may be referring to the broken hyperlink on the bioconductor website, http://bioconductor.org/packages/release/bioc/manuals/TCGAbiolinks/man/TCGAbiolinks.pdf/?

Until that is fixed, you can still access the vignettes here (files ending in .rmd): https://github.com/BioinformaticsFMRP/TCGAbiolinks/tree/master/vignettes

[cx-333]

Thank you for your kind help and other resolutions. But I still hope the broken website can be repaired as fast as possible.

[torongs82]

Hi @cx-333 , Xin Chen. First thank you in your interest in using or let's say try to understand how to use TCGAbiolinks first, and secondly , eventually to use it. But anyway, I am here to help you. Please can you clarify your message? What are you looking for? Are you referring to our vignette?

[cx-333]

Yeah, I want to use TCGAbiolinks package to generate BRCA for breast invasive carcinoma PAM50 subtype classification dataset. Due to the need of my research and the lack of corresponding sample ID, cohort of existing BRCA PAM50 subtype dataset, so I have to download BRCA data utilizing TCGABiolinks, process them, label each sample's subtype and other information by myself. Now I am first contact the R package and very eager for the relevant knowledge about it.

[torongs82]

Hi @cx-333 (Xin Chen), good morning. I assume that you understood that I visioned and with @tiagochst and other collaborators worked, and we are working a lot to keep the package functional active? I hope so. Anyway I got your clarification, I have to disagree with you about the missing of the TCGA-BRCA PAM50 molecular subtype annotation, it is there. You need just to look for it better. Please consider the following code: ``

[torongs82]

require(TCGAbiolinks) df_Subt <- as.data.frame(PanCancerAtlas_subtypes()) head(df_Subt)[,1:5] table(df_Subt$cancer.type) cancer <- "BRCA" dataSubt <- df_Subt[df_Subt$cancer.type %in% cancer,] head(dataSubt)[,1:5] table(dataSubt$cancer.type) table(dataSubt$Subtype_mRNA)

[torongs82]

Hi @cx-333 as you have time, can you try the code I wrote for you and let me know, if this helped? thank you.

[cx-333]

OK ! I feel free will try it in my computer and tell you the outcome of the code. Thank you very much.

[cx-333]

Wow, Thank you, the above code you offer can I run in my computer normally, and I obtain the pan.SamplesID, cancer.subtype as well as sample number information. This will be useful for my research. Maybe you resolve my problem perfectly, but I may meet some unseen problems in the future. So I just ask for the detailed usage of TCGAbiolinks package. I would appreciate it if you provide me service manual about it.

[tiagochst]

The manual is back in Bioconductor release version at https://bioconductor.org/packages/3.17/bioc/vignettes/TCGAbiolinks/inst/doc/index.html

[cx-333]

Thank you 🎉