# doseR

## Documentation for package ‘doseR’ version 1.29.0

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

## Help Pages

dafs | dafs
dafsFilter | dafsFilter Function to filter expression data within an object.
generateStats | generateStats Statistics function to summarize expression data of an s.e. object.
getLibsizes3 | getLibsizes3 Get Lib Sizes.
glSeq | glSeq LME4 wrapper.
hmel.dat | Hmel data set
iqrxFilter | iqrxFilter Function to filter expression data within an s.e. object.
make_RPKM | make_RPKM Make RPKM.
plotExpr | plotExpr Function to generate a boxplot (expression) for a SummarizedExperiment object based on the replicate data.
plotMA.se | plotMA.se Function to make MA plot.
plotRatioBoxes | plotRatioBoxes Function to boxplot density of ratios between two treatments (using groupings from an annotation column) within a SummarizedExperiment object.
plotRatioDensity | plotRatioDensity Function to plot density of ratios between two treatments (using groupings from an annotation column) within an object.
quantFilter | quantFilter Function to filter expression data of a SummarizedExperiment object.
se | Hmel data set
se.DM | se.DM Function to convert SummarizedExperiment object to LME4 input.
simpleFilter | simpleFilter Function to filter expression data of an object.
test_diffs | test_diffs Statistics function to summarize expression data of an object, using ratios between selected treatments.