search

BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
298 stars 112 forks source link

Question install and use TCGAbiolinks #31

Closed YangZX88 closed 8 years ago

YangZX88 commented 8 years ago

Hi, question with using packagesTCGAbiolinks, error like this: 1) when I use function GDCquery_Maf(), it appears: cannot open URL 'https://gdc-api.nci.nih.gov/data//abbe72a5-cb39-48e4-8df5-5fd2349f2bb2' 2) using TCGAquery_investigate(): could not find function "TCGAquery_investigate" I install the packages with order: biocLite("TCGAbiolinks"), is there any other packages need to install?

very thanks ! Yang

tiagochst commented 8 years ago

Hi,

1) I updated recently the method to download the Maf files, we had several connections problems this week and I tried to improve the code. However, the code is not in Bioconductor yet. Please, could you use the github version and see if it is working ? devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")

2) We just removed TCGAquery_Investigate (there was a difference in the name from the vignette and the code, sorry for that) and TGCA_profilePlot from the code. We had a problem with the limit size of the package and we had to prioritize some functions.

You're welcome, Tiago

YangZX88 commented 8 years ago

Hi, Tiago

It works with the new script,thanks!

But in running TCGAvisualize_oncoprint() commond, error like this:

[cid:397cffc0-ef39-4940-a95c-8274f3fcc94d]

BTW, commond : mut <- GDCquery_Maf(tumor = "ACC") must be handled, because mut can not be recognizes as an obj in R

Best

Yang

Yang Zhenxing

Department of Urology Xinqiao Hospital Third Military Medical University Chongqing, 400037, PR China

Tel:+86 18290442322 Fax: 023-68774453 yangzx88@hotmail.com

From: Tiago Chedraoui Silva notifications@github.com Sent: Thursday, September 29, 2016 2:46 PM To: BioinformaticsFMRP/TCGAbiolinks Cc: YangZX88; Author Subject: Re: [BioinformaticsFMRP/TCGAbiolinks] Question install and use TCGAbiolinks (#31)

Hi,

1) I updated recently the method to download the Maf files, we had several connections problems this week and I tried to improve the code. However, the code is not in Bioconductor yet. Please, could you use the github version and see if it is working ? devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")

2) We just removed TCGAquery_Investigate (there was a difference in the name from the vignette and the code, sorry for that) and TGCA_profilePlot from the code. We had a problem with the limit size of the package and we had to prioritize some functions.

You're welcome, Tiago

You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/31#issuecomment-250487900, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVeB-tn6K9qyYq9OxvF6sl97HNNmXc7gks5qu89MgaJpZM4KJhSv.

tiagochst commented 8 years ago

Hi,

I believe there is an image missing in the last post.

mut is a tibble object, it should be recognized. Does library(readr) works? 

> class(mut)
[1] "tbl_df"     "tbl"        "data.frame"

Best, Tiago

tiagochst commented 8 years ago

Hi,

Is this last version working for you?

devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")
library(TCGAbiolinks)
acc.muse.maf <- GDCquery_Maf("ACC", pipelines = "muse")

Best regards, Tiago

YangZX88 commented 8 years ago

Hi, Tiago,

It works,thanks!

Yang

Yang Zhenxing

Department of Urology Xinqiao Hospital Third Military Medical University Chongqing, 400037, PR China

Tel:+86 18290442322 Fax: 023-68774453 yangzx88@hotmail.com

From: Tiago Chedraoui Silva notifications@github.com Sent: Wednesday, November 2, 2016 10:22 PM To: BioinformaticsFMRP/TCGAbiolinks Cc: YangZX88; Author Subject: Re: [BioinformaticsFMRP/TCGAbiolinks] Question install and use TCGAbiolinks (#31)

Hi,

Is this last version working for you?

devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks") library(TCGAbiolinks) acc.muse.maf <- GDCquery_Maf("ACC", pipelines = "muse")

Best regards, Tiago

You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/31#issuecomment-258017640, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AVeB-sredpGWH-y8HBTWb5sYZyZhAhsVks5q6Q02gaJpZM4KJhSv.