/ppiAPMS

[Deprecated]Protein-protein interaction from AP-MS data (ppiAPMS) Please use SMAD(http://bioconductor.org/packages/release/bioc/html/SMAD.html)

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ppiAPMS[Deprecated]

This is an R package that implements statistical modeling approaches that assign confidence scores to protein-protein interaction data generated using affinity purification–mass spectrometry (AP-MS) data.Please use SMAD(http://bioconductor.org/packages/release/bioc/html/SMAD.html)

Installation

The development version can be installed through github:

 devtools::install_github(repo="zqzneptune/ppiAPMS")
 library(ppiAPMS)

Quick start

  1. CompPASS and CompPASS-Plus

Summarize your AP-MS data from proteome database search into the dataframe datInput with the following format:

idRun idBait idPrey countPrey
Unique ID of one AP-MS run Bait ID Prey ID Prey peptide count

Then run:

CompPASS(datInput)

CompPASSplus(datInput)
  1. HGScore

For datInput, we need more column 'lenPrey', while 'idBait' is not necessary:

idRun idPrey countPrey lenPrey
Unique ID of one AP-MS run Prey ID Prey peptide count Prey protein length

Then run:

HG(datInput)

License

MIT @ Qingzhou Zhang