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

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.

Author
Josh Bowden [aut], Jason Ross [aut, cre], Yalchin Oytam [aut]
Date of publication
None
Maintainer
Jason Ross <jason.ross@csiro.au>
License
GPL-3 + file LICENCE
Version
1.2.0
URLs

View on Bioconductor

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.

Files in this package

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