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Difference between revisions of "Programming/R"

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== Programming Details ==
 
== Programming Details ==
  
−
R is a programming language and software environment for statistical analysis, graphics representation and reporting.  
+
R is a programming language and software environment for statistical analysis, graphics representation, and reporting.  
  
−
R is freely available under the GNU General Public License, and can be loaded as a module on  Viper (with Linux), Windows (PC) and Mac.
+
R is freely available under the GNU General Public License and can be loaded as a module on  Viper (with Linux), Windows (PC), and Mac.
  
 
* R has versions 3.5.1 and R/4.0.2. (Earlier versions will be retired)
 
* R has versions 3.5.1 and R/4.0.2. (Earlier versions will be retired)
Line 35: Line 35:
 
====Batch Mode====
 
====Batch Mode====
  
−
The SLURM batch file would typical look like the one below, in this case it would be named ''''rscript.job''''.
+
The SLURM batch file would typically look like the one below, in this case, it would be named ''''rscript.job''''.
  
 
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
Line 47: Line 47:
 
#SBATCH -e %N.%j.%a.err
 
#SBATCH -e %N.%j.%a.err
 
#SBATCH -p compute
 
#SBATCH -p compute
 +
#SBATCH --mail-user= your email address here
  
 
echo $SLURM_JOB_NODELIST
 
echo $SLURM_JOB_NODELIST
Line 127: Line 128:
 
                         including modifying them to follow a particular
 
                         including modifying them to follow a particular
 
                         naming style
 
                         naming style
−
GenomeInfoDbData        Species and taxonomy ID look up tables used by
+
GenomeInfoDbData        Species and taxonomy ID lookup tables used by
 
                         GenomeInfoDb
 
                         GenomeInfoDb
 
GenomicAlignments      Representation and manipulation of short
 
GenomicAlignments      Representation and manipulation of short
Line 156: Line 157:
 
Rhtslib                HTSlib high-throughput sequencing library as an
 
Rhtslib                HTSlib high-throughput sequencing library as an
 
                         R package
 
                         R package
−
Rsamtools              Binary alignment (BAM), FASTA, variant call
+
Rsamtools              Binary alignment (BAM), FASTA, variant calling
 
                         (BCF), and tabix file import
 
                         (BCF), and tabix file import
 
S4Vectors              Foundation of vector-like and list-like
 
S4Vectors              Foundation of vector-like and list-like
Line 176: Line 177:
 
If you need an additional library installed that would be used by more than just yourself, contact the Viper team on [https://support.hull.ac.uk/ Topdesk]  with the details of the library and the version of R you require it for.
 
If you need an additional library installed that would be used by more than just yourself, contact the Viper team on [https://support.hull.ac.uk/ Topdesk]  with the details of the library and the version of R you require it for.
  
−
Alternatively, you can install a R library into your own personal library.  Within R run the install.packages command with the package you wish to install.
+
Alternatively, you can install an R library into your own personal library.  Within R run the install.packages command with the package you wish to install.
  
 
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
 
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">

Revision as of 09:18, 24 May 2021

Programming Details

R is a programming language and software environment for statistical analysis, graphics representation, and reporting.

R is freely available under the GNU General Public License and can be loaded as a module on Viper (with Linux), Windows (PC), and Mac.

  • R has versions 3.5.1 and R/4.0.2. (Earlier versions will be retired)

R-Studio is also provided as an interactive session on Viper for R-Studio.


Programming example


x <- c(151, 174, 138, 186, 128, 136, 179, 163, 152, 131)
y <- c(63, 81, 56, 91, 47, 57, 76, 72, 62, 48)

# Apply the lm() function.
relation <- lm(y~x)

print(relation)

Modules Available

The following modules are available:

  • module add R/3.4.1

Batch Mode

The SLURM batch file would typically look like the one below, in this case, it would be named 'rscript.job'. 


#!/bin/bash
#SBATCH -J compute-single-node
#SBATCH -N 1
#SBATCH --ntasks-per-node 1
#SBATCH -D /home/pysdlb/CODE_SAMPLES/R
#SBATCH -o %N.%j.%a.out
#SBATCH -e %N.%j.%a.err
#SBATCH -p compute
#SBATCH --mail-user= your email address here

echo $SLURM_JOB_NODELIST

module purge
module add R/3.4.1

export I_MPI_DEBUG=5
export I_MPI_FABRICS=shm:tmi
export I_MPI_FALLBACK=no

Rscript r.rsc

To run this on the cluster you would need to invoke the command sbatch rscript.job


Interactive Mode

The program is interpreted by the R runtime program, so compilation does not apply here. 


[pysdlb@login01 ~]$ interactive
salloc: Granted job allocation 3039458
Job ID 3039458 connecting to c120, please wait...
[pysdlb@c120 ~]$ module load R/4.0.2
[pysdlb@c120 ~]$ R

R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[Previously saved workspace restored]

>

Libraries

To show the libraries included type ( within R ) the command : library() 


Packages in library '/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library':

AnnotationDbi           Manipulation of SQLite-based annotations in
                        Bioconductor
BH                      Boost C++ Header Files
Biobase                 Biobase: Base functions for Bioconductor
BiocFileCache           Manage Files Across Sessions
BiocGenerics            S4 generic functions used in Bioconductor
BiocManager             Access the Bioconductor Project Package
                        Repository
BiocParallel            Bioconductor facilities for parallel evaluation
BiocStyle               Standard styles for vignettes and other
                        Bioconductor documents
BiocVersion             Set the appropriate version of Bioconductor
                        packages
Biostrings              Efficient manipulation of biological strings
DBI                     R Database Interface
DelayedArray            A unified framework for working transparently
                        with on-disk and in-memory array-like datasets
GenomeInfoDb            Utilities for manipulating chromosome names,
                        including modifying them to follow a particular
                        naming style
GenomeInfoDbData        Species and taxonomy ID lookup tables used by
                        GenomeInfoDb
GenomicAlignments       Representation and manipulation of short
                        genomic alignments
GenomicFeatures         Conveniently import and query gene models
GenomicRanges           Representation and manipulation of genomic
                        intervals
IRanges                 Foundation of integer range manipulation in
                        Bioconductor
KEGG.db                 A set of annotation maps for KEGG
KernSmooth              Functions for Kernel Smoothing Supporting Wand
                        & Jones (1995)
MASS                    Support Functions and Datasets for Venables and
                        Ripley's MASS
Matrix                  Sparse and Dense Matrix Classes and Methods
R6                      Encapsulated Classes with Reference Semantics
RColorBrewer            ColorBrewer Palettes
RCurl                   General Network (HTTP/FTP/...) Client Interface
                        for R
RNAseqData.HNRNPC.bam.chr14
                        Aligned reads from RNAseq experiment:
                        Transcription profiling by high throughput
                        sequencing of HNRNPC knockdown and control HeLa
                        cells
RSQLite                 'SQLite' Interface for R
RUnit                   R Unit Test Framework
Rcpp                    Seamless R and C++ Integration
Rhtslib                 HTSlib high-throughput sequencing library as an
                        R package
Rsamtools               Binary alignment (BAM), FASTA, variant calling
                        (BCF), and tabix file import
S4Vectors               Foundation of vector-like and list-like
                        containers in Bioconductor
SummarizedExperiment    SummarizedExperiment container
XML                     Tools for Parsing and Generating XML Within R
                        and S-Plus
XVector                 Foundation of external vector representation
                        and manipulation in Bioconductor
askpass                 Safe Password Entry for R, Git, and SSH
assertthat              Easy Pre and Post Assertions
:

Installing Additional Libraries

If you need an additional library installed that would be used by more than just yourself, contact the Viper team on Topdesk with the details of the library and the version of R you require it for.

Alternatively, you can install an R library into your own personal library. Within R run the install.packages command with the package you wish to install. 


> install.packages("R.matlab")
Warning in install.packages("R.matlab") :
  'lib = "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"' is not writable
Would you like to use a personal library instead?  (y/n) y
Would you like to create a personal library
~/R/x86_64-pc-linux-gnu-library/3.3
to install packages into?  (y/n) y
--- Please select a CRAN mirror for use in this session ---
HTTPS CRAN mirror

 1: 0-Cloud [https]                 2: Algeria [https]
 3: Australia (Canberra) [https]    4: Australia (Melbourne) [https]
 5: Australia (Perth) [https]       6: Austria [https]
 7: Belgium (Ghent) [https]         8: Brazil (RJ) [https]
 9: Brazil (SP 1) [https]          10: Bulgaria [https]
11: Canada (MB) [https]            12: Chile 1 [https]
13: Chile 2 [https]                14: China (Beijing) [https]
15: China (Hefei) [https]          16: China (Lanzhou) [https]
17: Colombia (Cali) [https]        18: Czech Republic [https]
19: Denmark [https]                20: France (Lyon 1) [https]
21: France (Lyon 2) [https]        22: France (Marseille) [https]
23: France (Montpellier) [https]   24: France (Paris 2) [https]
25: Germany (Münster) [https]      26: Iceland [https]
27: India [https]                  28: Indonesia (Jakarta) [https]
29: Ireland [https]                30: Italy (Padua) [https]
31: Japan (Tokyo) [https]          32: Malaysia [https]
33: Mexico (Mexico City) [https]   34: New Zealand [https]
35: Norway [https]                 36: Philippines [https]
37: Russia (Moscow) [https]        38: Serbia [https]
39: Spain (A Coruña) [https]       40: Spain (Madrid) [https]
41: Sweden [https]                 42: Switzerland [https]
43: Taiwan (Chungli) [https]       44: Turkey (Denizli) [https]
45: Turkey (Mersin) [https]        46: UK (Bristol) [https]
47: UK (Cambridge) [https]         48: UK (London 1) [https]
49: USA (CA 1) [https]             50: USA (IA) [https]
51: USA (IN) [https]               52: USA (KS) [https]
53: USA (MI 1) [https]             54: USA (OR) [https]
55: USA (TN) [https]               56: USA (TX 1) [https]
57: USA (TX 2) [https]             58: (HTTP mirrors)


Selection: 48
also installing the dependencies ‘R.methodsS3’, ‘R.oo’, ‘R.utils’

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/R.methodsS3_1.7.1.tar.gz'
Content type 'unknown' length 25731 bytes (25 KB)
==================================================
downloaded 25 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/R.oo_1.21.0.tar.gz'
Content type 'unknown' length 403410 bytes (393 KB)
==================================================
downloaded 393 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/R.utils_2.5.0.tar.gz'
Content type 'unknown' length 389402 bytes (380 KB)
==================================================
downloaded 380 KB

trying URL 'https://cran.ma.imperial.ac.uk/src/contrib/R.matlab_3.6.1.tar.gz'
Content type 'unknown' length 109818 bytes (107 KB)
==================================================
downloaded 107 KB

* installing *source* package ‘R.methodsS3’ ...
** package ‘R.methodsS3’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (R.methodsS3)
* installing *source* package ‘R.oo’ ...
** package ‘R.oo’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (R.oo)
* installing *source* package ‘R.utils’ ...
** package ‘R.utils’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
Warning in setGenericS3.default(name, export = exportGeneric, envir = envir,  :
  Renamed the preexisting function warnings to warnings.default, which was defined in environment base.
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (R.utils)
* installing *source* package ‘R.matlab’ ...
** package ‘R.matlab’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (R.matlab)

The downloaded source packages are in
        ‘/tmp/RtmpO7iqto/downloaded_packages’

Listing packages installed

If you need a package that will be used frequently visit Topdesk with your request.

To view those already installed within R 

> installed.packages()

AnnotationDbi               "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
BH                          "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
Biobase                     "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
BiocFileCache               "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
BiocGenerics                "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
BiocManager                 "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
BiocParallel                "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
BiocStyle                   "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
BiocVersion                 "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
Biostrings                  "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
DBI                         "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
DelayedArray                "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
GenomeInfoDb                "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
GenomeInfoDbData            "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
GenomicAlignments           "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
GenomicFeatures             "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
GenomicRanges               "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
IRanges                     "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
KEGG.db                     "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
KernSmooth                  "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
MASS                        "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
Matrix                      "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
R6                          "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
RColorBrewer                "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
RCurl                       "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
RNAseqData.HNRNPC.bam.chr14 "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
RSQLite                     "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
RUnit                       "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
Rcpp                        "/trinity/clustervision/CentOS/7/apps/R/4.0.2/lib64/R/library"
....


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