Exploratory Data Analysis of LC-MS/MS data by spectral counts
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Documentation for package ‘msmsEDA’ version 1.44.0
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 |