BwUniCluster2.0/Software/R/cummeRbund: Difference between revisions
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(Created page with "= General information = [https://rspatial.github.io/terra/ '''<code>CummeRbund</code>'''] is an <code>R</code> package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output. = Installation instructions = == Preparations == Installing <code>CummeRbund</code> involves compiling source code. Therefore, ensure that the following flags are set in <code>$HOME/.R/Makevars</code>: <pre> cat ~/.R/Makevars CXX14=g++ CXX17=g++ CXX14FLAGS += -std=c++14 C...") |
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= General information = |
= General information = |
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[https:// |
[https://compbio.mit.edu/cummeRbund/ '''<code>CummeRbund</code>'''] is an <code>R</code> package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output. |
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= Installation instructions = |
= Installation instructions = |
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== Preparations == |
== Preparations == |
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Installing <code>CummeRbund</code> involves compiling source code. Therefore, ensure that the following flags are set in <code>$HOME/.R/Makevars</code>: |
Installing <code>CummeRbund</code> involves compiling source code. Therefore, ensure that the following flags are set in <code>$HOME/.R/Makevars</code>: |
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module load math/R/4.4.1-mkl-2022.2.1-gnu-13.3 |
module load math/R/4.4.1-mkl-2022.2.1-gnu-13.3 |
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</pre> |
</pre> |
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== Install the R package == |
== Install the R package == |
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The <code>CummeRbund</code> package is not available from CRAN but can be installed from [https://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html '''BioConductor''']: |
The <code>CummeRbund</code> package is not available from CRAN but can be installed from [https://www.bioconductor.org/packages/release/bioc/html/cummeRbund.html '''BioConductor''']: |
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Latest revision as of 15:20, 30 October 2024
General information
CummeRbund is an R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output.
Installation instructions
Preparations
Installing CummeRbund involves compiling source code. Therefore, ensure that the following flags are set in $HOME/.R/Makevars:
cat ~/.R/Makevars CXX14=g++ CXX17=g++ CXX14FLAGS += -std=c++14 CXX17FLAGS += -std=c++17 CXXFLAGS = -O3 -fPIC -march=cascadelake -ffp-contract=off -fno-fast-math -fno-signed-zeros -fopenmp -Wno-unknown-warning-option
If necessary, the appropriate compiler flags can be set by running the following lines of code:
mkdir -p ~/.R echo "CXX14=g++" > ~/.R/Makevars echo "CXX17=g++" >> ~/.R/Makevars echo "CXXFLAGS = -O3 -fPIC -march=cascadelake -ffp-contract=off -fno-fast-math -fno-signed-zeros -fopenmp -Wno-unknown-warning-option" >> ~/.R/Makevars echo "CXX14FLAGS += -std=c++14" >> ~/.R/Makevars echo "CXX17FLAGS += -std=c++17" >> ~/.R/Makevars
Since installing glmnet involves compiling, we start an interactive session on one of the compute nodes:
salloc -n 1 -t 30 -p dev_single
From within the interactive session, load R 4.4.1:
module load math/R/4.4.1-mkl-2022.2.1-gnu-13.3
Install the R package
The CummeRbund package is not available from CRAN but can be installed from BioConductor:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cummeRbund")
Test the installation
As a quick test of the installation of CummeRbund the following lines of code can be run:
### R code from vignette source 'cummeRbund-example-workflow.Rnw'
###################################################
### code chunk number 1: init
###################################################
options(width=65)
###################################################
### code chunk number 2: loadLib
###################################################
library(cummeRbund)
###################################################
### code chunk number 3: read
###################################################
cuff <- readCufflinks(dir=system.file("extdata", package="cummeRbund"))
cuff
###################################################
### code chunk number 4: model_fit_1
###################################################
d<-dispersionPlot(genes(cuff))
d
###################################################
### code chunk number 5: model_fit_1_plot
###################################################
d<-dispersionPlot(genes(cuff))
d
print(d)
###################################################
### code chunk number 6: rep_boxplot_1
###################################################
pBoxRep<-csBoxplot(genes(cuff),replicates=T)
pBoxRep
###################################################
### code chunk number 7: rep_dendro_1
###################################################
pDendro<-csDendro(genes(cuff),replicates=T)
pDendro
###################################################
### code chunk number 8: rep_boxplot_1_plot
###################################################
pBoxRep<-csBoxplot(genes(cuff),replicates=T)
pBoxRep
print(pBoxRep)
###################################################
### code chunk number 9: rep_dendro_1_plot
###################################################
pDendro<-csDendro(genes(cuff),replicates=T)
pDendro
print(pDendro)
###################################################
### code chunk number 10: boxplot_1
###################################################
pBox<-csBoxplot(genes(cuff))
pBox
###################################################
### code chunk number 11: boxplot_1_plot
###################################################
pBox<-csBoxplot(genes(cuff))
pBox
print(pBox)
###################################################
### code chunk number 12: diff_exp_genes_1
###################################################
sigGeneIds<-getSig(cuff,alpha=0.05,level="genes")
head(sigGeneIds)
length(sigGeneIds)
###################################################
### code chunk number 13: diff_exp_genes_2
###################################################
hESCvsFibroblast.sigGeneIds<-getSig(cuff,"hESC","Fibroblasts",alpha=0.05,level="genes")
head(hESCvsFibroblast.sigGeneIds)
length(hESCvsFibroblast.sigGeneIds)
###################################################
### code chunk number 14: diff_exp_genes_3
###################################################
sigGenes<-getGenes(cuff,sigGeneIds)
sigGenes
###################################################
### code chunk number 15: diff_exp_feat_1
###################################################
sigGeneIds<-getSig(cuff,alpha=0.05,level="isoforms")
head(sigGeneIds)
length(sigGeneIds)
###################################################
### code chunk number 16: ind_gene_1
###################################################
Pink1<-getGene(cuff,'PINK1')
Pink1