RAPIDR: Reliable Accurate Prenatal non-Invasive Diagnosis R package
Version 0.1.1

Package to perform non-invasive fetal testing for aneuploidies using sequencing count data from cell-free DNA

Browse man pages Browse package API and functions Browse package files

AuthorKitty Lo <kitty.lo@ucl.ac.uk>
Date of publication2014-11-20 18:16:37
MaintainerKitty Lo <kitty.lo@ucl.ac.uk>
LicenseGPL-3
Version0.1.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("RAPIDR")

Man pages

BinBam: BinBam
createReferenceSetFromCounts: createReferenceSetFromCounts
evalPerformance: evalPerformance
gcContent: gcContent in 20kb bins
makeBinnedCountsFile: makeBinnedCountsFile
makeGCContentData: makeGCContentData
makeGCContentPerPos: makeGCContentPerPos
outcomes: set of simulated outcomes data
plotTestSample: plotTestSample
print.rapidr.ref: print.rapidr.ref
print.rapidr.test: print.rapidr.test
ReadBed: ReadBed
testUnknowns: testUnknowns
writeCleanedCountsFile: writeCleanedCountsFiles
writeResultsToFile: writeResultsToFile

Functions

BinBam Man page Source code
BinListOfBam Source code
ReadBed Man page Source code
aggregateCounts Source code
callUnknowns Source code
correct.counts.with.PCA Source code
createReferenceSetFromCounts Man page Source code
data.qc Source code
doPCA Source code
evalPerformance Man page Source code
find.chrY.excl.bins Source code
find.excl.bins Source code
findBaseline Source code
gcContent Man page
gcCorrectCounts Source code
gcCorrectOneSample Source code
gcCorrectOneSampleLoess Source code
makeBinnedCountsFile Man page Source code
makeGCContentData Man page Source code
makeGCContentPerPos Man page Source code
outcomes Man page
plotTestSample Man page Source code
print.rapidr.ref Man page Source code
print.rapidr.test Man page Source code
sum.counts Source code
testUnknowns Man page Source code
writeCleanedCountsFile Man page Source code
writeResultsToFile Man page Source code

Files

inst
inst/doc
inst/doc/rapidr-vignette.rnw
inst/doc/rapidr-vignette.pdf
inst/doc/rapidr-vignette.R
NAMESPACE
demo
demo/00Index
demo/doNIPT.R
NEWS
data
data/gcContent.rda
data/datalist
data/outcomes.rda
R
R/testUnknowns.R
R/helpFunctions.R
R/PCA.R
R/gcContent-data.R
R/print-methods.R
R/rapidr-package.R
R/outcomes-data.R
R/createReference.R
R/evalPerformance.R
vignettes
vignettes/rapidr-vignette.rnw
vignettes/workflow.png
MD5
build
build/vignette.rds
DESCRIPTION
man
man/testUnknowns.Rd
man/gcContent.Rd
man/makeGCContentPerPos.Rd
man/print.rapidr.test.Rd
man/writeCleanedCountsFile.Rd
man/plotTestSample.Rd
man/ReadBed.Rd
man/makeGCContentData.Rd
man/createReferenceSetFromCounts.Rd
man/print.rapidr.ref.Rd
man/evalPerformance.Rd
man/makeBinnedCountsFile.Rd
man/outcomes.Rd
man/BinBam.Rd
man/writeResultsToFile.Rd
RAPIDR documentation built on May 19, 2017, 8:12 a.m.