Dispersion shrinkage for sequencing data


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Documentation for package ‘DSS’ version 2.50.1

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DSS-package Dispersion shrinkage for sequencing data
callDML Function to detect differntially methylated loci (DML) from bisulfite sequencing (BS-seq) data.
callDMR Function to detect differntially methylated regions (DMR) from bisulfite sequencing (BS-seq) data.
design Experimental design for the example RRBS dataset
dispersion Acessor functions for the 'dispersion' slot in a SeqCountData object.
dispersion-method Acessor functions for the 'dispersion' slot in a SeqCountData object.
dispersion<- Acessor functions for the 'dispersion' slot in a SeqCountData object.
dispersion<--method Acessor functions for the 'dispersion' slot in a SeqCountData object.
DMLfit.multiFactor Fit a linear model for BS-seq data from general experimental design
DMLtest Function to perform statistical test of differntially methylated loci (DML) for two group comparisons of bisulfite sequencing (BS-seq) data.
DMLtest.multiFactor Perform statistical test for BS-seq data from general experimental design
DSS Dispersion shrinkage for sequencing data
DSS.DE Perform RNA-seq differential expression analysis in two-group comparison
estDispersion Estimate and shrink tag-specific dipsersions
estDispersion-method Estimate and shrink tag-specific dipsersions
estNormFactors Estimate normalization factors
estNormFactors-method Estimate normalization factors
makeBSseqData Create an object of BSseq class from several data frames.
newSeqCountSet Class '"SeqCountSet"' - container for count data from sequencing experiment
normalizationFactor Accessor functions for the 'normalizationFactor' slot in a SeqCountData object.
normalizationFactor-method Accessor functions for the 'normalizationFactor' slot in a SeqCountData object.
normalizationFactor<- Accessor functions for the 'normalizationFactor' slot in a SeqCountData object.
normalizationFactor<--method Accessor functions for the 'normalizationFactor' slot in a SeqCountData object.
RRBS An example dataset for multiple factor design
SeqCountSet Class '"SeqCountSet"' - container for count data from sequencing experiment
SeqCountSet-class Class '"SeqCountSet"' - container for count data from sequencing experiment
seqData A simulated 'SeqCountData' object.
showOneDMR Visualze the count data for one DMR
waldTest Perform gene-wise Wald test for two group comparisons for sequencing count data.
waldTest-method Perform gene-wise Wald test for two group comparisons for sequencing count data.