pepStat: Statistical analysis of peptide microarrays
Version 1.10.0

Statistical analysis of peptide microarrays

AuthorRaphael Gottardo, Gregory C Imholte, Renan Sauteraud, Mike Jiang
Bioconductor views Microarray Preprocessing
Date of publicationNone
MaintainerGregory C Imholte <gimholte@uw.edu>
LicenseArtistic-2.0
Version1.10.0
URL https://github.com/RGLab/pepStat
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("pepStat")

Popular man pages

baseline_correct: Substract baseline intensities
baselineCorrect.pSet: Substract baseline intensities
makePeptideSet: peptideSet constructor
normalizeArray: Normalize tiling array data using sequence information
peptideSet: peptideSet class
peptideSet-methods: peptideSet methods
slidingMean: Data smoothing for peptide microarray.
See all...

All man pages Function index File listing

Man pages

baseline_correct: Substract baseline intensities
baselineCorrect.pSet: Substract baseline intensities
create_db: Create a peptide collection
makeCalls: Make antibody binding positivity calls
makePeptideSet: peptideSet constructor
normalizeArray: Normalize tiling array data using sequence information
peptideSet: peptideSet class
peptideSet-methods: peptideSet methods
plotArray: Plot microarray images
restab: Result table
shinyPepStat: Launch the pepStat Shiny Application
slidingMean: Data smoothing for peptide microarray.
summarizePeptides: Add information to a peptideSet and summarize peptides

Functions

NormalizeArray Man page
[,peptideSet,ANY,ANY,ANY-method Man page
applySlidingMean Source code
baselineCorrect.pSet Man page Source code
baseline_correct Man page Source code
bgCorrect.pSet Source code
checkArgs_sumPeps Source code
check_peptideSet Source code
clade Man page
clade,GRanges-method Man page
clade,peptideSet-method Man page
clade-methods Man page
computeZpep Source code
create_db Man page Source code
end,peptideSet-method Man page
featureID Man page
featureID,peptideSet-method Man page
featureID-method Man page
findFDR Source code
getPlotCoords Source code
getPlotGrid Source code
getWeightedEstimator Source code
getZpep Source code
makeCalls Man page Source code
makePeptideSet Man page Source code
makeResiduals Source code
makeZpepMatrix Source code
normalizeArray Man page Source code
pepZscore Man page
pepZscore,GRanges-method Man page
pepZscore,peptideSet-method Man page
pepZscore-method Man page
pepZscore<- Man page
pepZscore<-,GRanges,data.frame-method Man page
pepZscore<-,peptideSet,data.frame-method Man page
peptide Man page
peptide,peptideSet-method Man page
peptide-method Man page
peptide<- Man page
peptide<-,peptideSet,character-method Man page
peptideSet Man page
peptideSet-class Man page
peptideSet-methods Man page
plotArrayImage Man page Source code
plotArrayResiduals Man page Source code
position Man page
position,peptideSet-method Man page
position-method Man page
ranges,peptideSet-method Man page
ranges<-,peptideSet-method Man page
restab Man page Source code
sanitize_mapping_file2 Source code
set_rownames Source code
shinyPepStat Man page Source code
show,peptideSet-method Man page
slidingMean Man page Source code
smoothResiduals Source code
start,peptideSet-method Man page
subset,peptideSet-method Man page
summarizePeptides Man page Source code
summary,peptideSet-method Man page
values,peptideSet-method Man page
width,peptideSet-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllMethods.R
R/create_db.R
R/import.R
R/internal.R
R/makeCalls.R
R/makePeptideSet.R
R/normalizeArray.R
R/plotArrayImage.R
R/results.R
R/shinyPepStat.R
R/slidingMean.R
R/summarizePeptides.R
build
build/vignette.rds
examples
examples/pipeline.R
inst
inst/doc
inst/doc/pepStat.R
inst/doc/pepStat.Rnw
inst/doc/pepStat.pdf
inst/shiny
inst/shiny/common_functions.R
inst/shiny/scripts.js
inst/shiny/server.R
inst/shiny/styles.css
inst/shiny/tooltips.js
inst/shiny/ui.R
inst/shiny/www
inst/shiny/www/opentip
inst/shiny/www/opentip/opentip-jquery.min.js
inst/shiny/www/opentip/opentip.css
man
man/baselineCorrect.pSet.Rd
man/baseline_correct.Rd
man/create_db.Rd
man/makeCalls.Rd
man/makePeptideSet.Rd
man/normalizeArray.Rd
man/peptideSet-methods.Rd
man/peptideSet.Rd
man/plotArray.Rd
man/restab.Rd
man/shinyPepStat.Rd
man/slidingMean.Rd
man/summarizePeptides.Rd
vignettes
vignettes/pepStat.Rnw
pepStat documentation built on May 20, 2017, 10:24 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.