msmsEDA: Exploratory Data Analysis of LC-MS/MS data by spectral counts

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Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors.

Author
Josep Gregori, Alex Sanchez, and Josep Villanueva
Date of publication
None
Maintainer
Josep Gregori <josep.gregori@gmail.com>
License
GPL-2
Version
1.12.0

View on Bioconductor

Man pages

batch.neutralize
Batch effects correction
counts.hc
Hierarchical clustering on an spectral counts matrix.
counts.heatmap
Heatmap of an spectral counts matrix.
counts.pca
Principal components analysis of an spectral counts matrix.
count.stats
Summary of statistics of spectral counts by sample in the...
disp.estimates
Residual dispersion estimates
filter.flags
Flag proteins with a minimum signal and/or sufficient...
gene.table
Gene symbols associated to protein accessions
msms.dataset
LC-MS/MS dataset
msmsEDA-package
Exploratory Data Analysis of label-free LC-MS/MS spectral...
norm.counts
Spectral counts matrix normalization
pnms
Accessions and gene symbols
pp.msms.data
Spectral counts matrix pre-processing
spc.barplots
Set of SpC barplots by sample
spc.boxplots
Set of SpC boxplots by sample
spc.densityplots
SpC density plots of a SpC matrix
spc.scatterplot
Scatterplot of SpC means comparing two conditions

Files in this package

msmsEDA/DESCRIPTION
msmsEDA/NAMESPACE
msmsEDA/R
msmsEDA/R/EDA_functions.R
msmsEDA/build
msmsEDA/build/vignette.rds
msmsEDA/data
msmsEDA/data/msms.dataset.rda
msmsEDA/data/pnms.rda
msmsEDA/inst
msmsEDA/inst/doc
msmsEDA/inst/doc/msmsData-Vignette.R
msmsEDA/inst/doc/msmsData-Vignette.Rnw
msmsEDA/inst/doc/msmsData-Vignette.pdf
msmsEDA/man
msmsEDA/man/batch.neutralize.Rd
msmsEDA/man/count.stats.Rd
msmsEDA/man/counts.hc.Rd
msmsEDA/man/counts.heatmap.Rd
msmsEDA/man/counts.pca.Rd
msmsEDA/man/disp.estimates.Rd
msmsEDA/man/filter.flags.Rd
msmsEDA/man/gene.table.Rd
msmsEDA/man/msms.dataset.Rd
msmsEDA/man/msmsEDA-package.Rd
msmsEDA/man/norm.counts.Rd
msmsEDA/man/pnms.Rd
msmsEDA/man/pp.msms.data.Rd
msmsEDA/man/spc.barplots.Rd
msmsEDA/man/spc.boxplots.Rd
msmsEDA/man/spc.densityplots.Rd
msmsEDA/man/spc.scatterplot.Rd
msmsEDA/vignettes
msmsEDA/vignettes/msmsData-Vignette.Rnw