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


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Documentation for package ‘msmsEDA’ version 1.44.0

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msmsEDA-package Exploratory Data Analysis of label-free LC-MS/MS spectral counts
batch.neutralize Batch effects correction
count.stats Summary of statistics of spectral counts by sample in the dataset
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.
disp.estimates Residual dispersion estimates
filter.flags Flag proteins with a minimum signal and/or sufficient dispersion.
gene.table Gene symbols associated to protein accessions
msms.dataset LC-MS/MS dataset
msmsEDA Exploratory Data Analysis of label-free LC-MS/MS spectral counts
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