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ggloor / ALDEx2_dev

ALDEx tool to examine compositional high-throughput sequence data with Welch's t-test
GNU Affero General Public License v3.0
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Implemented Bioconductor suggestions #2

Closed ruthgrace closed 10 years ago

ruthgrace commented 10 years ago

Changed version number to 0.99.2.

Implemented the following changes (this text is also in the NEWS document):

CHANGES IN VERSION 0.99.2

NEW FEATURES

o made aldex.clr into a class

o allowed input of SummarizedExperiment object instead of a reads data frame

o prioritized use of the BiocParallel package for multicore processing. If BiocParallel is not installed then the parallel package used, if neither packages are installed, then serial processing is used
ggloor commented 10 years ago

Awesome Ruth

I’ll check it out and get back to you

Greg

On Aug 28, 2014, at 1:47 PM, Ruth Grace Wong notifications@github.com wrote:

Changed version number to 0.99.2.

Implemented the following changes (this text is also in the NEWS document):

CHANGES IN VERSION 0.99.2

NEW FEATURES

o made aldex.clr into a class

o allowed input of SummarizedExperiment object instead of a reads data frame

o prioritized use of the BiocParallel package for multicore processing. If BiocParallel is not installed then the parallel package used, if neither packages are installed, then serial processing is used

You can merge this Pull Request by running

git pull https://github.com/ruthgrace/ALDEx2 master Or view, comment on, or merge it at:

https://github.com/ggloor/ALDEx2/pull/2

Commit Summary

• made a S4 class to define an aldex.clr type • added Methods to Depends in DESCRIPTION • added SummarizedExperiment functionality -- NOT TESTED • made version number 0.99.2, coded up usage of BiocParallel (NOT TESTED) • debugged overloading of aldex.clr class so that it takes in SummarizedExperiment or data frame for the read count table • debugged BiocParallel multi core option (names of data structures were not preserved with bplapply) File Changes

• A .DS_Store (0) • M ALDEx2/.DS_Store (0) • M ALDEx2/DESCRIPTION (4) • M ALDEx2/NAMESPACE (2) • M ALDEx2/NEWS (12) • A ALDEx2/R/AllClasses.R (34) • A ALDEx2/R/AllGenerics.R (21) • M ALDEx2/R/aldex.r (5) • M ALDEx2/R/clr_effect.r (20) • M ALDEx2/R/clr_function.r (87) • M ALDEx2/R/clr_glm.r (14) • M ALDEx2/R/clr_ttest.r (20) Patch Links:

• https://github.com/ggloor/ALDEx2/pull/2.patch • https://github.com/ggloor/ALDEx2/pull/2.diff — Reply to this email directly or view it on GitHub.

ruthgrace commented 10 years ago

Fixed documentation, so that everything works with R BUILD and R CHECK. Missing a vignette pdf.