apmsWAPP: Pre- and Postprocessing for AP-MS data analysis based on spectral counts

apmsWAPP provides a complete workflow for the analysis of AP-MS data (replicate single-bait purifications including negative controls) based on spectral counts. It comprises pre-processing, scoring and postprocessing of protein interactions. A final list of interaction candidates is reported: it provides a ranking of the candidates according to their p-values which allow estimating the number of false-positive interactions.

Author
Martina Fischer
Date of publication
2014-04-22 14:39:54
Maintainer
Martina Fischer <fischerm@rki.de>
License
LGPL-3
Version
1.0

View on CRAN

Man pages

apmsWAPP-internal
internal functions
apmsWAPP-package
Pre- and Postprocessing for AP-MS data analysis
int_mat
Format transformation of spectral counts
norm.inttable
Normalization of spectral count data
saint_permF
Pre- and Postprocessing for AP-MS data analysis using SAINT
tspm_apms
Workflow for AP-MS data analysis using TSPM
varFilter
Filtering of AP-MS data

Files in this package

apmsWAPP
apmsWAPP/inst
apmsWAPP/inst/extdata
apmsWAPP/inst/extdata/prottable.txt
apmsWAPP/inst/extdata/inttable.txt
apmsWAPP/inst/extdata/baittab.txt
apmsWAPP/NAMESPACE
apmsWAPP/R
apmsWAPP/R/TSPM_apms.r
apmsWAPP/R/Inttab_Norm.R
apmsWAPP/R/myWFalg_Dudoit.r
apmsWAPP/R/mat_Int_change.r
apmsWAPP/R/NonspecFilter.r
apmsWAPP/R/saint_permF.r
apmsWAPP/R/Saintout_process.r
apmsWAPP/R/myTSPM.r
apmsWAPP/MD5
apmsWAPP/DESCRIPTION
apmsWAPP/man
apmsWAPP/man/varFilter.Rd
apmsWAPP/man/apmsWAPP-package.Rd
apmsWAPP/man/norm.inttable.Rd
apmsWAPP/man/apmsWAPP-internal.Rd
apmsWAPP/man/saint_permF.Rd
apmsWAPP/man/int_mat.Rd
apmsWAPP/man/tspm_apms.Rd