# Dispersion shrinkage for sequencing data

## Documentation for package ‘DSS’ version 2.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.