Collection of functions for reading and comparing SAGE libraries


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Documentation for package ‘sagenhaft’ version 1.12.0

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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