Man pages for ramwas
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... |
