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.

Install the latest version of this package by entering the following in R:
install.packages("msarc")
AuthorGord Brown, Hisham Mohammed
Date of publication2015-01-27 16:55:53
MaintainerGord Brown <gdbzork@gmail.com>
LicenseArtistic-2.0
Version1.4.5

View on CRAN

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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