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msmsEDA (version 1.10.0)

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

Description

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

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Version

Version

1.10.0

License

GPL-2

Maintainer

Josep Gregori

Last Published

February 15th, 2017

Functions in msmsEDA (1.10.0)

counts.heatmap

Heatmap of an spectral counts matrix.
filter.flags

Flag proteins with a minimum signal and/or sufficient dispersion.
msmsEDA-package

Exploratory Data Analysis of label-free LC-MS/MS spectral counts
spc.densityplots

SpC density plots of a SpC matrix
norm.counts

Spectral counts matrix normalization
spc.scatterplot

Scatterplot of SpC means comparing two conditions
pp.msms.data

Spectral counts matrix pre-processing
batch.neutralize

Batch effects correction
pnms

Accessions and gene symbols
msms.dataset

LC-MS/MS dataset
counts.pca

Principal components analysis of an spectral counts matrix.
disp.estimates

Residual dispersion estimates
count.stats

Summary of statistics of spectral counts by sample in the dataset
gene.table

Gene symbols associated to protein accessions
counts.hc

Hierarchical clustering on an spectral counts matrix.
spc.boxplots

Set of SpC boxplots by sample
spc.barplots

Set of SpC barplots by sample