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 |
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 | Extract Data (Coverage) Matrix Columns by Genomic Location |
getTestsByLocation | Extract MWAS Test Results by Genomic Location |
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. |
makefullpath | Combine Path and Filename into Filename with Path |
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 |
plotROC | Plot ROC Curve. |
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 |
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 |
testPhenotype | Test the Phenotype of Interest for Association with Methylation Coverage. |