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

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.

AuthorGord Brown, Hisham Mohammed
Date of publication2015-01-27 16:55:53
MaintainerGord Brown <gdbzork@gmail.com>
LicenseArtistic-2.0
Version1.4.5

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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

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