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brge_data_large's Introduction

BRGEdata

BRGEdata in a data-R package that includes a collection of BRGE omic and exposome data.

Data available in this R package:

Data Type Number of Samples Number of Features Technology File Name Object Name Class
Exposome 110 15 brge_expo.rda brge_expo ExposomeSet
Transcriptome 100 67528 Affymetrix HTA 2.0 brge_gexp.rda brge_gexp ExpressionSet
Methylome 20 476946 Illumina Human Methylation 450K brge_methy.rda brge_methy GenomicRatioSet
Proteome 90 47 brge_prot.rda brge_prot ExpressionSet

The phenotype data corresponding to the samples was included in each set:

  • sex
  • age

Moreover, the ExposomeSet includes:

  • asthma status
  • rhinitis status

The following table indicates the source of each class includeid in BRGdata data-R package:

Class Source
ExposomeSet rexposome
ExpressionSet Biobase
GenomicRatioSet minfi

brge_data_large's People

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carleshf avatar dpelegri avatar escri11 avatar isglobal-brge avatar leireabarrategui avatar yocra3 avatar

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brge_data_large's Issues

Errors in Bioconductor Build System (BBS)

Hi Carles, @carleshf @isglobal-brge

Please check the build report below and address any issues with the experiment data package.
https://bioconductor.org/checkResults/3.7/data-experiment-LATEST/brgedata/malbec2-buildsrc.html

Warning: file ‘brge_expo.rda’ has magic number 'versi'
  Use of save versions prior to 2 is deprecated
Error in load(zfile, envir = envir) : 
  bad restore file magic number (file may be corrupted) -- no data loaded
ERROR: lazydata failed for package ‘brgedata’

Your omicRexposome package is candidate for deprecation. Please resolve these issues
as soon as possible for your continued inclusion in Bioconductor.

Best regards,
Marcel

how to solve the problem, thanks in advance

devtools::install_local("/home/sheyu/Downloads/omic1/brgedata-master.zip")
Skipping 1 packages ahead of CRAN: formatR
Installing package into ‘/home/sheyu/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)

  • installing source package ‘brgedata’ ...
    ** using staged installation
    ** R
    ** data
    *** moving datasets to lazyload DB
    Warning: file ‘asthma.rda’ has magic number 'versi'
    Use of save versions prior to 2 is deprecated
    Error in load(zfile, envir = tmp_env) :
    bad restore file magic number (file may be corrupted) -- no data loaded
    ERROR: lazydata failed for package ‘brgedata’
  • removing ‘/home/sheyu/R/x86_64-pc-linux-gnu-library/3.6/brgedata’
    Error: Failed to install 'brgedata-master.zip' from local:
    (converted from warning) installation of package ‘/tmp/RtmpQoSJ4q/remotes1c764cde52e9/brgedata-master’ had non-zero exit status

Cannot read obesity.bed file

I am using brgedata version 1.10.0 with R version 4.0.2 on Ubuntu 18.04.
I am trying to use read.plink with the obesity files (which are not available in the directory of the package, so I downloaded them manually from the GitHub repository). The problem is that when I try to read obesity.bed I receive the following error message:

Error in scan(..., :
line 1 did not have 3 elements

Any suggestion? Thank you. @isglobal-brge

No metabolite names in the metabol_serum.Rdata file

Hi, I download the metabol_serum/metabol_urine.Rdata files, and found there is no metabolite names in metabol_serum.Rdata file, only the classe information. And there is metabolite information (name, ID etc) in metabol_urine@featureData@data.

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