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. |