# Collection of functions for reading and comparing SAGE libraries

## Documentation for package `sagenhaft' version 1.4.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

combine.libs | Functions for SAGE library extraction
compare.lib.pair | Class sage.library.comparison
compute.sequence.neighbors | Estimate sequencing errors and compute corrected counts
compute.unique.tags | Functions for SAGE library extraction
create.matrix.csr | Utilities
difference.scatter.plot | Utilities
em.estimate.error.given | Estimate sequencing errors and compute corrected counts
estimate.errors.mean | Estimate sequencing errors and compute corrected counts
extract.ditags | Functions for SAGE library extraction
extract.lib.from.directory | Functions for SAGE library extraction
extract.lib.from.zip | Functions for SAGE library extraction
extract.library.tags | Functions for SAGE library extraction
plot.sage.library | Class sage.library
plot.sage.library.comparison | Class sage.library.comparison
print.sage.library | Class sage.library
print.sage.library.comparison | Class sage.library.comparison
read.phd.file | Functions for SAGE library extraction
read.sage.library | Class sage.library
read.sage.library.comparison | Class sage.library.comparison
read.seq.qual.filepair | Functions for SAGE library extraction
reestimate.lib.from.tagcounts | Functions for SAGE library extraction
remove.sage.artifacts | Functions for SAGE library extraction
revcomp | Utilities
sage.test | Compare Two SAGE Libraries
SAGEartifacts | Functions for SAGE library extraction
sagelibrary.simulate | Simulate SAGE libraries
summary.sage.library | Class sage.library
summary.sage.library.comparison | Class sage.library.comparison
table.sparse | Utilities
tagmatrix2tagnum | Utilities
tagnum2tagmatrix | Utilities
tagnum2tagsequence | Utilities
tagsequence2tagnum | Utilities
write.sage.library | Class sage.library
write.sage.library.comparison | Class sage.library.comparison