Harman: The removal of batch effects from datasets using a PCA and constrained optimisation based technique
Version 1.4.0

Harman is a PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user.

Browse man pages Browse package API and functions Browse package files

AuthorJosh Bowden [aut], Jason Ross [aut, cre], Yalchin Oytam [aut]
Bioconductor views BatchEffect DNAMethylation Microarray MultipleComparison Normalization Preprocessing PrincipalComponent Software StatisticalMethod Transcription
Date of publicationNone
MaintainerJason Ross <jason.ross@csiro.au>
LicenseGPL-3 + file LICENCE
Version1.4.0
URL http://www.bioinformatics.csiro.au/harman/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Harman")

Man pages

arrowPlot: PCA before and after arrow plot for harman results
callHarman: Wrapper function to call the shared C/C++ library code
detachHarman: Detach the Harman package and its shared C/C++ library code
harman: Harman batch correction method
harmanresults: Harman results object
harmanScores: A Principal components prcomp function tweaked for Harman
pcaPlot: PCA plot for harman results
plot.harmanresults: Plot method for harman
prcompPlot: PCA plot
print.summary.harmanresults: Printing Harmanresults summaries.
reconstructData: Reconstruct corrected data from Harman results
shiftBetas: Shift beta values from 0 and 1 to avoid infinite M values
summary.harmanresults: Summarizing harman results.

Functions

.callHarman Man page
arrowPlot Man page Source code
callHarman Man page Source code
detachHarman Man page Source code
harman Man page Source code
harmanScores Man page Source code
harmanresults Man page
onUnload Source code
pcaPlot Man page Source code
plot.harmanresults Man page Source code
prcompPlot Man page Source code
print.summary.harmanresults Man page Source code
reconstructData Man page Source code
shiftBetas Man page Source code
summary.harmanresults Man page Source code

Files

DESCRIPTION
Harman.Rproj
LICENCE
NAMESPACE
R
R/Harman.R
R/arrowPlot.R
R/callHarman.R
R/detachHarman.R
R/harmanScores.R
R/harmanresults.R
R/pcaPlot.R
R/plot.harmanresults.R
R/prcompPlot.R
R/reconstructData.R
R/shiftBetas.R
R/summary.harmanresults.R
R/zzz.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/IntroductionToHarman.R
inst/doc/IntroductionToHarman.Rmd
inst/doc/IntroductionToHarman.html
inst/extdata
inst/extdata/NPM_data_first_1000_rows.csv.gz
inst/extdata/NPM_info.csv.gz
inst/unitTests
inst/unitTests/test_R_layer.R
inst/unitTests/test_Rcpp_layer.R
man
man/arrowPlot.Rd
man/callHarman.Rd
man/detachHarman.Rd
man/harman.Rd
man/harmanScores.Rd
man/harmanresults.Rd
man/pcaPlot.Rd
man/plot.harmanresults.Rd
man/prcompPlot.Rd
man/print.summary.harmanresults.Rd
man/reconstructData.Rd
man/shiftBetas.Rd
man/summary.harmanresults.Rd
src
src/CMapSelectKFromN.h
src/CSelectRandom.h
src/Harman.cpp
src/Makevars
src/Makevars.win
tests
tests/runTests.R
vignettes
vignettes/IntroductionToHarman.Rmd
Harman documentation built on May 20, 2017, 11:02 p.m.