/usr/lib/R/site-library/GenomeInfoDb/NEWS is in r-bioc-genomeinfodb 1.6.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 | CHANGES IN VERSION 0.99.1
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SIGNIFICANT USER-VISIBLE CHANGES
o The Seqnames package will have functions which will be moved from
AnnotationDbi , GenomicRanges
o List of 9 functions moved from AnnotationDbi
supportedSeqnameMappings, findSequenceRenamingMaps,
supportedSeqnameStyles, supportedSeqnames,
extractSeqnameSet, testSeqnames, isSupportedSeqnamesStyle,
listAllSupportedStylesBySpecies, listAllSupportedSeqnameStyles.
o makeSeqnameIds moved from GenomicRanges
o keepStandardChromosomes moved from GenomicRanges
o rename:
keepStandardChromosomes -> keepChromosomes
NEW FEATURES
o added new functions:
supportedOrganisms()
supportedSeqnameMappingsWithGroup()
extractSeqnameSetByGroup()
CHANGES IN VERSION 0.99.6
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NEW FEATURES
o add new functions()
seqnamesInGroup which will take a character vector of chromosomes and
return the chromosomes specified by the group parameter supplied by the
user. The user can also give the species and the style.
seqnamesOrder() internally calls Herve's function makeSeqnameIds()
o add seqnameStyles generic and method from GenomicRanges
SIGNIFICANT USER-VISIBLE CHANGES
o rename:
testSeqnames -> isSupportedSeqnames
o move SeqnamesStyle generic from GenomicRanges and define a new method which
works on a character vector.
DEPRECATED AND DEFUNCT
o deprecate listAllSupportedStylesBySpecies(),
listAllSupportedSeqnameStyles(), supportedOrganisms()
supportedSeqnameMappingsWithGroup()
DEPRECATED AND USED INTERNALLY(NOT EXPORTED)
o deprecate supportedSeqnameMappings(), supportedSeqnameStyles(),
isSupportedSeqnamesStyle(),issupportedSeqnames()
CHANGES IN VERSION 0.99.7
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SIGNIFICANT USER-VISIBLE CHANGES
o rename:
isSupportedSeqnames -> .isSupportedSeqnames
supportedSeqnameStyles -> .supportedSeqnameStyles
supportedSeqnameMappings -> .supportedSeqnameMappings
isSupportedSeqnamesStyle -> .isSupportedSeqnamesStyle
CHANGES IN VERSION 0.99.14
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SIGNIFICANT USER-VISIBLE CHANGES
o rename:
package: Seqnames --> GenomeInfoDb
supportedStyles -> genomeStyles
makeSeqnameIds --> rankSeqlevels (add to export)
seqnamesOrder --> orderSeqlevels
extractSeqnameSet -> extractSeqlevels
extractSeqnameSetByGroup -> extractSeqlevelsByGroup
findSequenceRenamingMaps --> mapSeqlevels
seqnamesInGroup --> seqlevelsInGroup
seqnamesStyle --> seqlevelsStyle
"seqnameStyle<-" --> "seqlevelsStyle<-"
CHANGES IN VERSION 0.99.17
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SIGNIFICANT USER-VISIBLE CHANGES
o keepStandardChromosomes: Make 'species' argument optional and remove
'style' argument.
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