Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

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Documentation for package ‘ramwas’ version 1.33.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

ramwas-package	Fast Methylome-wide Association Study Pipeline for Enrichment Platforms
cachedRDSload	Cached Loading of RDS Files
colSumsSq	Form Row and Column Sums of Squares
estimateFragmentSizeDistribution	Estimate and plot Fragment Size Distribution.
findBestNpvs	Quickly Find N Smallest P-values in a Long Vector
getCpGsetALL	Construct CpG set for a Reference Genome
getCpGsetCG	Construct CpG set for a Reference Genome
getDataByLocation	Functions for Access to Data, MWAS Results, and Location Information
getLocations	Functions for Access to Data, MWAS Results, and Location Information
getMWAS	Functions for Access to Data, MWAS Results, and Location Information
getMWASandLocations	Functions for Access to Data, MWAS Results, and Location Information
getMWASrange	Functions for Access to Data, MWAS Results, and Location Information
injectSNPsMAF	Inject SNPs from VCF Count File into a DNA Sequence
insilicoFASTQ	Construct FASTQ File for In-silico Alignment Experiment
isAbsolutePath	Check if Path is Absolute.
madeBED	Export MWAS results in BED format.
madeBEDgraph	Export MWAS results in BED format.
madeBEDgraphRange	Export MWAS results in BED format.
madeBEDrange	Export MWAS results in BED format.
makefullpath	Combine Path and Filename into Filename with Path
manPlotFast	Fast Manhattan plot for Large Number of P-values
manPlotPrepare	Fast Manhattan plot for Large Number of P-values
mat2cols	Split a Matrix into Column Vectors
orthonormalizeCovariates	Orthonormalize Covariates
parameterDump	Save Parameters in a Text File
parameterPreprocess	Preprocess Pipeline Parameter List.
parametersFromFile	Scan Parameters From a R Code File
pipeline	RaMWAS: High Level Pipeline Functions
pipelineProcessBam	RaMWAS: High Level Pipeline Functions
plot.qcCoverageByDensity	Quality Control Measures
plot.qcEditDist	Quality Control Measures
plot.qcEditDistBF	Quality Control Measures
plot.qcHistScore	Quality Control Measures
plot.qcHistScoreBF	Quality Control Measures
plot.qcIsoDist	Quality Control Measures
plot.qcLengthMatched	Quality Control Measures
plot.qcLengthMatchedBF	Quality Control Measures
plotCVcors	Plotting Functions used in Cross Validation Analysis (Methylation Risk Score).
plotFragmentSizeDistributionEstimate	Estimate and plot Fragment Size Distribution.
plotPCvalues	Plot Principal component (PC) Values (variation explained) and PC vectors (loadings)
plotPCvectors	Plot Principal component (PC) Values (variation explained) and PC vectors (loadings)
plotPrediction	Plotting Functions used in Cross Validation Analysis (Methylation Risk Score).
plotROC	Plotting Functions used in Cross Validation Analysis (Methylation Risk Score).
processCommandLine	Scan Parameters From Command Line
pvalue2qvalue	Calculate Benjamini-Hochberg q-values
qcmean	Quality Control Measures
qcmean.NULL	Quality Control Measures
qcmean.qcChrX	Quality Control Measures
qcmean.qcChrY	Quality Control Measures
qcmean.qcCoverageByDensity	Quality Control Measures
qcmean.qcEditDist	Quality Control Measures
qcmean.qcEditDistBF	Quality Control Measures
qcmean.qcFrwrev	Quality Control Measures
qcmean.qcHistScore	Quality Control Measures
qcmean.qcHistScoreBF	Quality Control Measures
qcmean.qcIsoDist	Quality Control Measures
qcmean.qcLengthMatched	Quality Control Measures
qcmean.qcLengthMatchedBF	Quality Control Measures
qcmean.qcNonCpGreads	Quality Control Measures
qqPlotFast	Fast QQ-plot for Large Number of P-values
qqPlotPrepare	Fast QQ-plot for Large Number of P-values
ramwas	Fast Methylome-wide Association Study Pipeline for Enrichment Platforms
ramwas0createArtificialData	Create Artificial Data Set
ramwas1scanBams	RaMWAS: High Level Pipeline Functions
ramwas2collectqc	RaMWAS: High Level Pipeline Functions
ramwas3normalizedCoverage	RaMWAS: High Level Pipeline Functions
ramwas4PCA	RaMWAS: High Level Pipeline Functions
ramwas5MWAS	RaMWAS: High Level Pipeline Functions
ramwas6annotateTopFindings	RaMWAS: High Level Pipeline Functions
ramwas7ArunMWASes	RaMWAS: High Level Pipeline Functions
ramwas7BrunElasticNet	RaMWAS: High Level Pipeline Functions
ramwas7CplotByNCpGs	RaMWAS: High Level Pipeline Functions
ramwas7riskScoreCV	RaMWAS: High Level Pipeline Functions
ramwasAnnotateLocations	Extract Biomart Annotation for a Vector of Locations.
ramwasParameters	Function for Convenient Filling of the RaMWAS Parameter List.
ramwasSNPs	RaMWAS: High Level Pipeline Functions
rowSumsSq	Form Row and Column Sums of Squares
rwDataClass	Class for Accessing Data (Coverage) Matrix
rwDataClass-class	Class for Accessing Data (Coverage) Matrix
subsetCoverageDirByLocation	Subset a data matrix and locations
testPhenotype	Test the Phenotype of Interest for Association with Methylation Coverage.