[R] Efficient way of loading files in R

[Deepa]

I am also providing the output that I obtain for your kind reference,

gseEset2 <- getGEO('GSE76896', destdir = "data/")[[1]]
Found 1 file(s)
GSE76896_series_matrix.txt.gz
Using locally cached version: /data//GSE76896_series_matrix.txt.gz
Parsed with column specification:
cols(
  .default = col_double(),
  ID_REF = col_character()
)
See spec(...) for full column specifications.
Using locally cached version of GPL570 found here:
/data//GPL570.soft

After this I don't see any output. I had to forcefully stop the execution.

On Fri, Sep 7, 2018 at 4:05 PM Deepa <deepamahm.iisc using gmail.com> wrote:

> I already posted a similar issue on bioconductor.
> https://support.bioconductor.org/p/112607/#112634
> Couldn't find a solution.
>
>
> On Fri, Sep 7, 2018 at 3:45 PM Martin Morgan <mtmorgan.bioc using gmail.com>
> wrote:
>
>> Ask on the Bioconductor support site https://support.bioconductor.org
>>
>> Provide (on the support site) the output of the R commands
>>
>>    library(GEOquery)
>>    sessionInfo()
>>
>> Also include (copy and paste) the output of the command that fails. I have
>>
>>  > gseEset2 <- getGEO('GSE76896')[[1]]
>> Found 1 file(s)
>> GSE76896_series_matrix.txt.gz
>> trying URL
>> '
>> https://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76896/matrix/GSE76896_series_matrix.txt.gz
>> '
>> Content type 'application/x-gzip' length 40561936 bytes (38.7 MB)
>> ==================================================
>> downloaded 38.7 MB
>>
>> Parsed with column specification:
>> cols(
>>    .default = col_double(),
>>    ID_REF = col_character()
>> )
>> See spec(...) for full column specifications.
>> |=================================================================| 100%
>>    84 MB
>> File stored at:
>> /tmp/Rtmpe4NWji/GPL570.soft
>> |=================================================================| 100%
>>    75 MB
>>  > sessionInfo()
>> R version 3.5.1 Patched (2018-08-22 r75177)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 16.04.5 LTS
>>
>> Matrix products: default
>> BLAS: /home/mtmorgan/bin/R-3-5-branch/lib/libRblas.so
>> LAPACK: /home/mtmorgan/bin/R-3-5-branch/lib/libRlapack.so
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>> [1] bindrcpp_0.2.2      GEOquery_2.49.1     Biobase_2.41.2
>> [4] BiocGenerics_0.27.1 BiocManager_1.30.2
>>
>> loaded via a namespace (and not attached):
>>   [1] Rcpp_0.12.18     tidyr_0.8.1      crayon_1.3.4     dplyr_0.7.6
>>   [5] assertthat_0.2.0 R6_2.2.2         magrittr_1.5     pillar_1.3.0
>>   [9] stringi_1.2.4    rlang_0.2.2      curl_3.2         limma_3.37.4
>> [13] xml2_1.2.0       tools_3.5.1      readr_1.1.1      glue_1.3.0
>> [17] purrr_0.2.5      hms_0.4.2        compiler_3.5.1   pkgconfig_2.0.2
>> [21] tidyselect_0.2.4 bindr_0.1.1      tibble_1.4.2
>>
>> On 09/07/2018 06:08 AM, Deepa 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.
>> >
>>
>

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