Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

cachedRDSload | Cached Loading of RDS Files |

findBestNpvs | Quickly Find N Smallest P-values in a Long Vector |

get | Functions for Access to Data, MWAS Results, and Location... |

getCpGset | Construct CpG set for a Reference Genome |

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. |

MakeBED | Export MWAS results in BED format. |

makefullpath | Combine Path and Filename into Filename with Path |

manhattan | 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 |

plotCV | Plotting Functions used in Cross Validation Analysis... |

plotFragmentSizeDistributionEstimate | Estimate and plot Fragment Size Distribution. |

plotPC | Plot Principal component (PC) Values (variation explained)... |

processCommandLine | Scan Parameters From Command Line |

pvalue2qvalue | Calculate Benjamini-Hochberg q-values |

QCs | Quality Control Measures |

qqplotFast | Fast QQ-plot for Large Number of P-values |

RaMWAS | Fast Methylome-wide Association Study Pipeline for Enrichment... |

ramwas0createArtificialData | Create Artificial Data Set |

ramwasAnnotateLocations | Extract Biomart Annotation for a Vector of Locations. |

ramwasParameters | Function for Convenient Filling of the RaMWAS Parameter List. |

rowcolSumSq | Form Row and Column Sums of Squares |

rwDataClass-class | Class for Accessing Data (Coverage) Matrix |

subsetData | Subset a data matrix and locations |

testPhenotype | Test the Phenotype of Interest for Association with... |

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