# Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

## Documentation for package ‘ramwas’ version 1.10.0

- 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.