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NEWS
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# All changes to RNAModR are documented here
## Version 0.2.5
- Fixed issue #8 which affected showing enrichment plots with certain
`binWidth` to `posMax` values
- Changed the default multiple hypothesis testing correction to Bonferroni to
be more conservative
## Version 0.2.4
- Added option to have variable windows in `PlotRelDistDistribution`,
`PlotRelDistEnrichment`, `PlotRelStartStopEnrichment` (closes issue #6)
## Version 0.2.3
- In `plot.R`: Added `plotOverlap`
- In `helper.R`: `LoadRefTx` now performs version checks on the major, minor
and patch version level
- Added `extdata.R` with details on and references to all internal raw datasets
## Version 0.2.2
- In `plot.R`: Added `PlotRelStartStopEnrichment`
- In `helper.R`: Added `GetTxRegionCoordinates` and `GetDistNearestStartStop`;
these functions are needed by `PlotRelStartStopEnrichment`
## Version 0.2.1
- `BuildTx` now adds a `package_version` attribute to every transcriptome data
object
- Transcriptome data is now consistently loaded and verified using function
`LoadRefTx`; verification includes comparing the `package_version` attribute
and the current RNAModR package version. If there is a mismatch, a warning
is produced
## Version 0.2.0
- RNAModR now requires R >= 3.5.0
- Major changes to functions in buildTxMethods.R to reflect critical changes in
`GenomicRanges_1.32.0` and `RMariaDB` that completely broke functionality
of `BuildTx`
- Major changes to structure of `txLoc` objects; `txLoc` is now a dressed
`list` of `DataFrame`s (instead of a dressed `list` of `data.frame`s). This
has the advantage that we can now store arbitrary R objects in columns, such
as `GRanges`, `DNAStringSet` etc.
- In `classes.R`: Added `txLoc` S4 class method `show`; this means that we can
simply type the name of the `txLoc` object into an R terminal, hit <Enter>
and get a summary
- In `classes.R`: Removed `info` method
- In `classes.R`: Added `txLoc` S4 class method `GetRegions`
- In `classes.R`: Tidied roxygen2 documentation; all `txLoc` accessors are now
document under `txLoc-accessors` in the reference manual
- In `IO.R`: Renamed `WriteTxLocToBED` to `WriteBED`; chromosome names are
now always formatted in UCSC style (i.e. chr1, chr2, chrM, ...)
- In `IO.R`: Renamed `WriteTxLocToCSV` to `WriteCSV`
- In `IO.R`: Removed `WriteFeatToBED` and removed `rtracklayer` dependecy
- In `IO.R`: Removed `ReadDBN` (which was needed by `GetMFE`, which in turn
has also been removed)
- In `methods.R`: Removed `method = "perm"` from `GenerateNull`
- In `methods.R`: Removed `GetMFE`, because such functions should be managed
and defined on a per-use and per-user basis
- In `methods.R`: Removed `filter` argument from `GetMotifLoc`; this is
because filtering should be done through `FilterTxLoc`
- In `methods.R`: Removed `GenerateNull.new`, as it was a function for testing
purposes and served no real purpose
- In `methods.R`: Removed `GetLocus.MapFromTranscripts`, as it served no
purpose
- In `methods.R`: Refactored and tidied `GetGC`
- In `plot.R`: Removed `filter` argument from `PlotSectionDistribution`,
`PlotSpatialDistribution`, `PlotSectionEnrichment`, `PlotSpatialEnrichment`,
`PlotGC`; this is because filtering should be done through `FilterTxLoc`
- In `plot.R`: Removed `PlotTxSecLength`, `PlotTxSecLength.bean` and
`PlotOverlap`, because such functions should be managed and defined on a
per-use and per-user basis
- In `plot.R`: Refactored and tidied `PlotSectionDistribution`
- In `plot.R`: Refactored and tidied `PlotSectionEnrichment`
- In `plot.R`: Refactored and tidied `PlotSpatialEnrichment`
- In `helper.R`: Added `DownsampleTxLoc`; `DownsampleTxLoc` is a function that
downsamples the number of sites from on `txLoc` object to the number of sites
from a second `txLoc` object; downsampling is transcript region specific
- In `helper.R`: Tidied and refactored `SubsampleTxLoc`; `SubsampleTxLoc`
generates a subsample of sites per transcript region, based on a vector of
fractions
- In `helper.R`: Removed `internal` keyword from `FilterTxLoc`,
`SubsampleTxLoc`
- In `helper.R`: Refactored and tidied `FilterTxLoc`
- In `helper.R`: Fixed bug in `CheckClassTxLocConsistency` that prevented the
function from producing an error when regions did not match
- In `helper.R`: Removed `filter` argument from `TxLoc2GRangesList`; this is
because filtering should be done through `FilterTxLoc`
- In `helper.R`: `GetRelDistNearest` and `TxLoc2GRangesList` are now no
longer exported; this is because these functions should really never be
called directly by user.
- Renamed "transcript sections" to "transcript regions" in all documentation
- Fixed "no visible binding for global variable <xyz>" issues that derive from
`with(..., x = xyz)` statements by setting `xyz <- NULL` (this is the
recommended `data.table` way)
- DESCRIPTION: Added `Encoding: UTF-8` to silence R CMD check and roxygen2 from
complaining about encoding
## Version 0.1.0
- Changed method to calculate nearest distances between two
GRanges objects. We now collapse ranges to the start position
and determine nearest distances based on start positions of the
two GRanges objects. Thanks to Andrew Shafik for prompting this.