function is superseded by the
as the edgeR DGEList object structure changed
easyRNASeq function is superseded by the
simpleRNASeq function to consolidate and
prune the overall package. The changes are based on user comments and on the
general standardization occuring in the field.
fetchCoverage function only had two
parameters deprecated as the consequence of the package consolidation. As the scanBam
function is not called directly anymore but through higher level functions (from the
GenomicRanges package), the 'what' and 'isUnmappedQuery' parameters were obsolete.
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