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| 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. |