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

(Keeping the devel mailing list in the loop, so that  others with 
similar questions / answers can benefit / contribute)
I tested your first solution (View(studies)). I added it to the end of 
my code and everything worked perfectly. Do think I can use it this way 
or I have to write instruction for the users (vignette) to run it themself?
in the vignette you could give the user a taste for what they'll see 
with `head()` in an evaluated chunk, and mention that they could use 
`View()` in a non-evaluated chunk, something like

   ```{r}
   x = ...
   head(x)
   ```

To explore this object interactively, try

   ```{r, eval=FALSE}
   View(x)
   ```

Martin
Best regards,

Arman

*From: *Martin Morgan <mailto:martin.morgan at roswellpark.org>
*Sent: *Saturday, September 9, 2017 00:34
*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 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

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

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) {
      stopifnot(
          is.character(url), length(url) == 1L, nzchar(url),
          !is.na(url),
          is.character(query), length(query) == 1L, nzchar(query),
          !is.na(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()

Martin

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

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

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