Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms


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Documentation for package ‘ramwas’ version 1.0.0

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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
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.