msarc: Draw Diagrams (mis)Representing the Results of Mass Spec Experiments

Share:

The output of an affinity-purification mass spectrometry experiment is typically a list of proteins that were observed in the experiment, identified by UniProt identifiers (http://www.uniprot.org/). This package takes as input a list of UniProt identifiers, and the associated Mascot scores from the experiment (which indicate the likelihood that the protein has been correctly identified), clusters them by gene ontology category (http://geneontology.org/), then draws diagrams showing the results in hierarchical clusters by category, with lines for individual proteins representing the associated Mascot score. The results are in general not publication-ready, but will rather require editing via a graphics editor that can interpret SVG (scalable vector graphics) format. As an alternative representation, the package will also generate tag clouds based on the Mascot scores.

Author
Gord Brown, Hisham Mohammed
Date of publication
2015-01-27 16:55:53
Maintainer
Gord Brown <gdbzork@gmail.com>
License
Artistic-2.0
Version
1.4.5

View on CRAN

Man pages

msarc
Create msarc Object From Data Frame
msarc.copyColors
Copy 'msarc' Color Palette
msarc.findGOterms
Map UniProt Ids to GO Terms
msarc.loadMS
Create msarc Object From Mass Spec Data
msarc.loadTerms
Manipulate GO Term Lists
msarc-package
msarc: Mass Spectrometry Experiment Plots
msarc.plotCircle
Draw 'msarc' Diagram without GO categories
msarc.plotHeatmap
Correlation Heat Maps for Mass Spec Experiments
msarc.plotSVG
Draw 'msarc' Diagram
msarc.subtract
Subtract Control From Experiment
msarc.tagCloud
Draw Tag Cloud
print.msarc
Display an 'msarc' Object
sample_data
Sample Data for the msarc Package
sample_objects
Sample Objects for the msarc Package

Files in this package

msarc
msarc/inst
msarc/inst/CITATION
msarc/inst/extdata
msarc/inst/extdata/sample_colnames.txt.gz
msarc/inst/extdata/sample_msdata.txt.gz
msarc/inst/doc
msarc/inst/doc/msarc.R
msarc/inst/doc/msarc.pdf
msarc/inst/doc/msarc.Rnw
msarc/exec
msarc/exec/msarc_heatmap
msarc/exec/msSubtract.py
msarc/exec/msSummarize.py
msarc/exec/README
msarc/exec/msarc_part1
msarc/exec/msarc_part2
msarc/NAMESPACE
msarc/data
msarc/data/sample_subtracted.rda
msarc/data/sample_initial.rda
msarc/data/sample_df.txt.gz
msarc/data/control_initial.rda
msarc/data/sample_cluster.rda
msarc/data/control_df.txt.gz
msarc/data/sample_complete.rda
msarc/data/sample_goterms.rda
msarc/R
msarc/R/msarc.R
msarc/R/plotter.R
msarc/R/cluster.R
msarc/R/loader.R
msarc/R/heatmap.R
msarc/vignettes
msarc/vignettes/samplePlot.png
msarc/vignettes/msarc_bib.bib
msarc/vignettes/msarc.Rnw
msarc/MD5
msarc/build
msarc/build/vignette.rds
msarc/DESCRIPTION
msarc/man
msarc/man/print.msarc.Rd
msarc/man/sample_data.Rd
msarc/man/msarc.findGOterms.Rd
msarc/man/msarc.tagCloud.Rd
msarc/man/msarc.copyColors.Rd
msarc/man/msarc.Rd
msarc/man/msarc.loadTerms.Rd
msarc/man/msarc.subtract.Rd
msarc/man/msarc.loadMS.Rd
msarc/man/msarc.plotSVG.Rd
msarc/man/msarc-package.Rd
msarc/man/sample_objects.Rd
msarc/man/msarc.plotHeatmap.Rd
msarc/man/msarc.plotCircle.Rd