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

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

## Documentation for package ‘msmsEDA’ version 1.51.0

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

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