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Fri, 09 May 2008
Ringo
some updates, mostly for improved handling ChIP-chip data generated on two-color Agilent arrays
Ringo
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Ringo
fixed a few typos in package man pages
Ringo
fixed an inconsistency in function 'findChersOnSmoothed' that can occur with certain values supplied for its argument 'cellType'
Ringo
improvements to preprocessing functions and extended README on example data
Ringo
minor updates following up on introduction of S4 classes for probeAnno and ChIP-enriched regions
and fixed a small bug in chromosomeNames method of probeAnno class
Ringo
updated vignette and graphviz script to handle S4 cher objects
Ringo
converted 'probeAnno' and 'ChIP-enriched region' into S4 classes, which also required some consecutive minor changes to other functions
Ringo
added another way of estimating the threshold for probe levels under ChIP-enrichment as suggested by Richard Bourgon
Ringo
modified function chipAlongChrom such that labels of genomic features (partly) contained in the displayed region are shown even when their start or end position is not contained
Ringo
many minor improvements and clarifications
Ringo
consistently replaced misleading term 'peak' by more appropriate one 'ChIP-enriched region'
Ringo
fixed bug in new function computeSlidingT
Ringo
a few minor changes to resolve inconstencies
Ringo
added new function to compute sliding t statistics and changed some logistics regarding the C functions
Ringo
improvements to functions for computing overlap between enriched regions and/or ovelap of genomic features and probe-mapped positions
Ringo
Region overlap matrices now use the matrix.csr representation from package SparseM. Other functions needed small follow-up changes because of this change.
Ringo
improved handling of identified enriched regions and fixed bug introduced in previous version
Ringo
fixed bug in function posToProbeAnno
added arguments for users to handle uniqueness of probe matches
Ringo
minor changes, mostly naming related
Ringo
Removed support for soon to be defunct class exprSet.
Ringo
Fixed a typo in the help file title. (Changed exprSet to ExpressionSet since that is what the function returns.)
Ringo
added a function to compute overlap between genomic regions in one set with those from another set
Ringo
added functionality and documentation for simplifying work with the probeAnno environment
Ringo
minor changes to VSN-related part of preprocessing functions that were made necessary by changes to the VSN package
Ringo
updated citation details