# Complexome Profiling Analysis package

## Documentation for package ‘ComPrAn’ version 1.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

allPeptidesPlot | Create scatter plot
assignClusters | Create a data frames with cluster assignment
cleanData | Clean raw peptide complexomics data
clusterComp | Create components necessary for clustering
compranApp | Execute the complexomics Shiny app
exportClusterAssignments | Covert clustered tables into format for export
extractRepPeps | Extract Only Data Belonging to Representative Peptide
getNormTable | Get normalised table for all proteins
groupHeatMap | Make heatmap
makeBarPlotClusterSummary | Title
makeDist | Make disstance matrix
normalizeTable | Convert extractRepPeps output to a Matrix
normTableForExport | Convert Normalized Dataframe to Export format
normTableWideToLong | Convert Normalized Dataframe To Long format
oneGroupTwoLabelsCoMigration | Compare a Single Group of Proteins Between Two Label States
onlyInOneLabelState | Report Proteins Present In Only One Label State
peptideImport | Import raw peptide complexomics data
pickPeptide | Select Top Peptide For Various Scenarios
proteinPlot | Create Line Plots
protImportForAnalysis | Modify import protein data
simplifyProteins | Simplify Raw Proteins file
splitModLab | Split Modification and Label tags
toFilter | Optional Filtering For Raw Data
twoGroupsWithinLabelCoMigration | Compare a Two Groups of Proteins Within One Label State
uncenteredCor | Perform uncentered correlation