ramwas-package	RaMWAS
cachedRDSload	cachedRDSload
colSumsSq	rowcolSumSq
estimateFragmentSizeDistribution	plotFragmentSizeDistributionEstimate
findBestNpvs	findBestNpvs
getCpGsetALL	getCpGset
getCpGsetCG	getCpGset
getDataByLocation	get
getLocations	get
getMWAS	get
getMWASandLocations	get
getMWASrange	get
injectSNPsMAF	injectSNPsMAF
insilicoFASTQ	insilicoFASTQ
isAbsolutePath	isAbsolutePath
madeBED	MakeBED
madeBEDgraph	MakeBED
madeBEDgraphRange	MakeBED
madeBEDrange	MakeBED
makefullpath	makefullpath
manPlotFast	manhattan
manPlotPrepare	manhattan
mat2cols	mat2cols
orthonormalizeCovariates	orthonormalizeCovariates
parameterDump	parameterDump
parameterPreprocess	parameterPreprocess
parametersFromFile	parametersFromFile
pipeline	pipeline
pipelineProcessBam	pipeline
plot.qcCoverageByDensity	QCs
plot.qcEditDist	QCs
plot.qcEditDistBF	QCs
plot.qcHistScore	QCs
plot.qcHistScoreBF	QCs
plot.qcIsoDist	QCs
plot.qcLengthMatched	QCs
plot.qcLengthMatchedBF	QCs
plotCVcors	plotCV
plotFragmentSizeDistributionEstimate	plotFragmentSizeDistributionEstimate
plotPCvalues	plotPC
plotPCvectors	plotPC
plotPrediction	plotCV
plotROC	plotCV
processCommandLine	processCommandLine
pvalue2qvalue	pvalue2qvalue
qcmean	QCs
qcmean.NULL	QCs
qcmean.qcChrX	QCs
qcmean.qcChrY	QCs
qcmean.qcCoverageByDensity	QCs
qcmean.qcEditDist	QCs
qcmean.qcEditDistBF	QCs
qcmean.qcFrwrev	QCs
qcmean.qcHistScore	QCs
qcmean.qcHistScoreBF	QCs
qcmean.qcIsoDist	QCs
qcmean.qcLengthMatched	QCs
qcmean.qcLengthMatchedBF	QCs
qcmean.qcNonCpGreads	QCs
qqPlotFast	qqplotFast
qqPlotPrepare	qqplotFast
ramwas	RaMWAS
ramwas0createArtificialData	ramwas0createArtificialData
ramwas1scanBams	pipeline
ramwas2collectqc	pipeline
ramwas3normalizedCoverage	pipeline
ramwas4PCA	pipeline
ramwas5MWAS	pipeline
ramwas6annotateTopFindings	pipeline
ramwas7ArunMWASes	pipeline
ramwas7BrunElasticNet	pipeline
ramwas7CplotByNCpGs	pipeline
ramwas7riskScoreCV	pipeline
ramwasAnnotateLocations	ramwasAnnotateLocations
ramwasParameters	ramwasParameters
ramwasSNPs	pipeline
rowSumsSq	rowcolSumSq
rwDataClass	rwDataClass-class
rwDataClass-class	rwDataClass-class
subsetCoverageDirByLocation	subsetData
testPhenotype	testPhenotype
