NEWS
metagenomeSeq 1.25
- Added 'wrenchNorm' function
- Added option to use IHW as p-value adustment method in 'MRcoefs'
- Modified 'expSummary' slot in 'MRexperiment' object to be of class 'list' instead of 'environment'
- Added results classes for 'fitZig' and 'fitFeatureModel' results
metagenomeSeq 1.21
- Numerous changes. Added greater flexibility to fitFeatureModel
metagenomeSeq 1.15
- Added 'mergeMRexperiment' function
- Added 'normFactors' and 'libSize' generics
- Added 'fitMultipleTimeSeries' function
- Replaced RUnit with testthat library for unit testing
- Adding multiple upgrades and changes throughout
- Deprecated the load_* functions and created load* function.
metagenomeSeq 1.13
- Upgrade support for biom-format vs. 2.0
- Fixed issue - "MRtable, etc will report NA rows when user requests more features than available"
- Fixed s2 miscalculation in calcZeroComponent
metagenomeSeq 1.11
- Adding fitFeatureModel - a feature based zero-inflated log-normal model.
- Added MRcoefs,MRtable,MRfulltable support for fitFeatureModel output.
- Added mention in vignette.
- Added support for normalizing matrices instead of just MRexperiment objects.
- Fixed cumNormStat's non-default qFlag option
metagenomeSeq 1.9
- Added flexibility in formula choice for fitTimeSeries
- Added readability in ssPermAnalysis
- Fixed default in plotClassTimeSeries (include = c("1",...))
- Added fitTimeSeries vignette
- Removed interactiveDisplay to namespace - moved to suggests
- Fixed ordering of MRtable,MRfulltable first four columns
- modified df estimated through responsibilities
- renamed fitMeta to fitLogNormal - a more appropriate name
metagenomeSeq 1.7 (2014-05-07)
- Added function plotBubble
- Added parallel (multi-core) options to fitPA, fitDO
- Fixed bug for fitMeta when useCSSoffset=FALSE and model matrix ncol==2
- (1.7.10) Updated default quantile estimate (.5) for low estimates
- (1.7.10) Added short description on how to do multiple group comparisons
- (1.7.15) Output of fitZig (eb) is now a result of limma::eBayes instead of limma::ebayes
- (1.7.16) plotMRheatmap allows for sorting by any stat (not just sd)
- (1.7.18) fitTimeSeries Including times series method for differentially abundant time intervals
- (1.7.20) Fixed minor bug for OTU level time series analyses and added plotClassTimeSeries
- (1.7.26) Added warning / fix if any samples are empty in cumNormStat
- (1.7.27) Added a few unit tests
- (1.7.29) Added interactiveDisplay to namespace (display function allows interactive exploration / plots through browser)
metagenomeSeq 1.5 (2014-04-17)
- Incorporating biom-format support with the biom2MRexperiment, MRexperiment2biom and load_biome function.
- Added uniqueFeatures, filterData, aggregateByTaxonomy / aggTax, plotFeature and calculateEffectiveSamples functions.
- Renamed MRfisher to fitPA (presence-absence fisher test).
- Added warnings for normalization
- Added fitDO (Discovery odds ratio test) and fitMeta (original metastats).
- Added match.call() info to fitZig output
- Fixed missing E-Step bounds
metagenomeSeq 1.2 (2013-08-20)
- Our paper got accepted and is available!
- Added methods for MRexperiment objects (colSums,colMeans,rowSums,rowMeans, usage is for example colSums(obj) or colSums(obj,norm=TRUE)) (09-25)
- Added two new functions, plotOrd and plotRare - a function to plot PCA/MDS coordinates and rarefaction effect (09-04,09-18)
- Updated MRfisher to include thresholding for presence-absence testing (08-19)
- Updated comments (roxygen2) style for all the functions using the Rd2roxygen package (07-13)
- Updated plotCorr and plotMRheatmap to allow various colors/not require trials(07-13)
- Rewrote vignette (and switched to knitr)
metagenomeSeq 1.1 (2013-06-25)
- Rewrote load_meta and load_metaQ to be faster/use less memory
- Modified cumNormStat to remove NA samples from calculations (example would be samples without any counts)
- Re-added plotGenus' jitter
- Fixed uniqueNames call in the MR tables
- Changed thanks to Kasper Daniel Hansen's suggestions the following:
plotOTU and plotGenus both have much better auto-generated axis
MRtable, MRfulltable, MRcoefs have a sort by p-value option now
MRtable, MRfulltable, MRcoefs now have an extra option to include unique numbers for OTU features (default would automatically add them previously)
cumNorm.R - now returns the object as well - not just replacing the environment
0 Still need to turn the fitZig output to S3, consider subsetting function address low p-values
metagenomeSeq 1.0.0 (2013-03-29)