cachedRDSload           Cached Loading of RDS Files
findBestNpvs            Quickly Find N Smallest P-values in a Long
                        Vector
getCpGsetCG             Construct CpG set for a Reference Genome
getLocations            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.
makefullpath            Combine Path and Filename into Filename with
                        Path
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
plotFragmentSizeDistributionEstimate
                        Estimate and plot Fragment Size Distribution.
plotPCvalues            Plot Principal component (PC) Values (variation
                        explained) and PC vectors (loadings)
plotPrediction          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
qqPlotFast              Fast QQ-plot for Large Number of P-values
ramwas-package          Fast Methylome-wide Association Study Pipeline
                        for Enrichment Platforms
ramwas0createArtificialData
                        Create Artificial Data Set
ramwasAnnotateLocations
                        Extract Biomart Annotation for a Vector of
                        Locations.
ramwasParameters        Function for Convenient Filling of the RaMWAS
                        Parameter List.
rowSumsSq               Form Row and Column Sums of Squares
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.
