[Bioc-devel] How can I remove limit of row numbers that can be printed on console?

Martin Morgan martin.morgan at roswellpark.org
Fri Sep 8 22:04:32 CEST 2017

On 09/08/2017 03:50 PM, Arman Shahrisa wrote:
> Thank you very much for helping. I have a package in Bioconductor 
> submission procedure.
> One of package functions shows the available cancer studies, allowing 
> the user to choose
> from them.  I have two options: Saving the output to the package 
> directory or printing it
> on the console. Apparently, assigning the output to environment is not 
> allowed,
> unless user does it by arrow sign him/her self (To me, both look like 
> the same!).
> Therefore, I have to print the output on console. I’ve seen such 
> approach in *cgdsr *package
> without any truncation. I took a look through its R code and couldn’t 
> figure it out. I thought
> maybe somebody knows what to do?
> My function also stores an excel file with the same output (to shre it 
> with others ). There is no
> logics behind saving the excel file and then opening it with R. So, I 
> think at the same time results
> should be stored as a variable or printed on console.

One way of using cgdsr is like

   cbiop <- CGDS("http://www.cbioportal.org/public-portal/")
   studies = getCancerStudies(cbiop)

does that fit your needs?

Another approach is to provide a simple way for the user to get more 
relevant data, for instance

queryStudies <- function(url, query) {
         is.character(url), length(url) == 1L, nzchar(url),
         is.character(query), length(query) == 1L, nzchar(query),
     cbiop <- CGDS(url)
     studies = getCancerStudies(cbiop)
     idx = Reduce(`|`, lapply(studies, grepl, pattern=query))
     if (sum(idx) > 1000)
         stop("'query' returned > 1000 matches; be more specific")
     studies[idx, , drop=FALSE]

used as

     > mystudies = queryStudies(url, "brca"))
     > dim(mystudies)
     [1] 9 3

which is very easy to work with, e.g., View()


> Best wishes,
> Arman
> *From: *Martin Morgan <mailto:martin.morgan at roswellpark.org>
> *Sent: *Friday, September 8, 2017 23:48
> *To: *Arman Shahrisa <mailto:shahrisa.arman at hotmail.com>; bioc-devel 
> <mailto:bioc-devel at r-project.org>
> *Subject: *Re: [Bioc-devel] How can I remove limit of row numbers that 
> can be printed on console?
> On 09/08/2017 02:11 PM, Arman Shahrisa wrote:
>> Hi everyone,
>> How can I prevent the R from truncating the printed result on console? I have to
>> print the output on console and I can�t use options(max.print = 10000) in my
>> function. What else I can do?
> this isn't really the right forum for base R questions (the r-help
> mailing list or StackOverflow might be more appropriate), but since you
> ask on the wrong forum ;), maybe I'll ask about why you'd want to print
> that much information to the console? you're not really going to read
> through it, are you?
> Martin
>> Sincerely
>> Arman
>>        [[alternative HTML version deleted]]
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