msarc: Draw Diagrams (mis)Representing the Results of Mass Spec Experiments
Version 1.4.5

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
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("msarc")

Getting started

Package overview

Popular man pages

msarc: Create msarc Object From Data Frame
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
sample_data: Sample Data for the msarc Package
sample_objects: Sample Objects for the msarc Package
See all...

All man pages Function index File listing

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

Functions

addGoAncestors Source code
addOneAncestorSet Source code
assignKidsToParents Source code
augmentGOlist Source code
control_df Man page
control_initial Man page
countOthers Source code
draw.arc.set Source code
draw.arcs Source code
draw.blind.scores Source code
draw.footer Source code
draw.header Source code
draw.missing Source code
draw.scores Source code
draw.tag Source code
extract.symbols Source code
filterGo Source code
filterUniprotInXref Source code
findAngle Source code
getBestGoCat Source code
getLowestGoCats Source code
getMissing Source code
getOthers Source code
getSmallest Source code
getSmallestGoCat Source code
go2table Source code
index2letters Source code
invertCats Source code
invertGOlist Source code
listmax Source code
listsum Source code
makeHierarchy Source code
makeTable Source code
mergeByName Source code
msarc Man page Source code
msarc-package Man page
msarc.copyColors Man page Source code
msarc.filterTerms Man page Source code
msarc.findGOterms Man page Source code
msarc.getTerms Man page Source code
msarc.loadMS Man page Source code
msarc.loadTerms Man page Source code
msarc.plotCircle Man page Source code
msarc.plotHeatmap Man page Source code
msarc.plotSVG Man page Source code
msarc.saveTerms Man page Source code
msarc.subtract Man page Source code
msarc.tagCloud Man page Source code
oneUniprot2go Source code
parentInList Source code
print.msarc Man page Source code
r2d Source code
read.nested Source code
sample_cluster Man page Man page
sample_complete Man page
sample_df Man page
sample_goterms Man page
sample_initial Man page
sample_subtracted Man page
setCandidates Source code
summary.msarc Man page Source code
topLevel Source code
treeDepth Source code
uniprot2go Source code
uniprotInTree Source code
write.arc Source code
write.background Source code
write.label Source code
write.separator Source code

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
msarc documentation built on May 19, 2017, 11:22 p.m.

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