Collection of functions for reading and comparing SAGE libraries

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Documentation for package ‘sagenhaft’ version 1.79.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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