msmsEDA: Exploratory Data Analysis of LC-MS/MS data by spectral counts
Version 1.14.0

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

AuthorJosep Gregori, Alex Sanchez, and Josep Villanueva
Bioconductor views MassSpectrometry Proteomics Software
Date of publicationNone
MaintainerJosep Gregori <josep.gregori@gmail.com>
LicenseGPL-2
Version1.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("msmsEDA")

Getting started

Package overview

Popular man pages

batch.neutralize: Batch effects correction
counts.pca: Principal components analysis of an spectral counts matrix.
count.stats: Summary of statistics of spectral counts by sample in the...
filter.flags: Flag proteins with a minimum signal and/or sufficient...
gene.table: Gene symbols associated to protein accessions
msmsEDA-package: Exploratory Data Analysis of label-free LC-MS/MS spectral...
norm.counts: Spectral counts matrix normalization
See all...

All man pages Function index File listing

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

Functions

Files

DESCRIPTION
NAMESPACE
R
R/EDA_functions.R
build
build/vignette.rds
data
data/msms.dataset.rda
data/pnms.rda
inst
inst/doc
inst/doc/msmsData-Vignette.R
inst/doc/msmsData-Vignette.Rnw
inst/doc/msmsData-Vignette.pdf
man
man/batch.neutralize.Rd
man/count.stats.Rd
man/counts.hc.Rd
man/counts.heatmap.Rd
man/counts.pca.Rd
man/disp.estimates.Rd
man/filter.flags.Rd
man/gene.table.Rd
man/msms.dataset.Rd
man/msmsEDA-package.Rd
man/norm.counts.Rd
man/pnms.Rd
man/pp.msms.data.Rd
man/spc.barplots.Rd
man/spc.boxplots.Rd
man/spc.densityplots.Rd
man/spc.scatterplot.Rd
vignettes
vignettes/msmsData-Vignette.Rnw
msmsEDA documentation built on May 20, 2017, 10:15 p.m.

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