[R] Efficient way of loading files in R

[Amit Mittal]

getgeo() seems to be a custom routine. Import the file in reader and
confirm that's a CSV file from Excel. If this is a non standard input,
custom subroutine is creating new constraints. Usually R has no problem
till workspace is 1 gb

On Fri 7 Sep, 2018, 15:38 Deepa, <deepamahm.iisc using gmail.com> wrote:

> Hello,
>
> I am using a bioconductor package in R.
> The command that I use reads the contents of a file downloaded from a
> database and creates an expression object.
>
> The syntax works perfectly fine when the input size is of 10 MB. Whereas,
> when the file size is around 40MB the object isn't created.
>
> Is there an efficient way of loading a large input file to create the
> expression object?
>
> This is my code,
>
>
> library(gcrma)
> library(limma)
> library(biomaRt)
> library(GEOquery)
> library(Biobase)
> require(GEOquery)
> require(Biobase)
> gseEset1 <- getGEO('GSE53454')[[1]] #filesize 10MB
> gseEset2 <- getGEO('GSE76896')[[1]] #file size 40MB
>
> ##gseEset2 doesn't load and isn't created
>
> Many thanks
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
-- 

______________________________

Amit Mittal
Pursuing Ph.D. in Finance and Accounting
Indian Institute of Management, Lucknow
Visit my SSRN author page:
http://ssrn.com/author=2665511
* Top 10% Downloaded Author on SSRN
Mob: +91 7525023664

This message has been sent from a mobile device. I may contact you again.

_________________

	[[alternative HTML version deleted]]