Changelog
Source:NEWS.md
myTAI 1.0.2.9000
New Functions
- New function
tfPS()
: Perform transformation of phylostratum values, analogous toPS()
which transforms expression levels. Currently,tfPS()
supports quantile rank transformation. - New function
PairwiseTest()
: Statistically evaluate the pairwise difference in the phylotranscriptomic pattern between two contrasts based on or computations. - New function
pairScore()
: Compute pairwise difference in TAI (or TDI) score.
myTAI 1.0.1.9000
New Functions
New function
PlotSignatureTransformed()
: Plot evolutionary signatures across transcriptomes and RNA-seq transformationsNew function
tfStability()
: Perform Permutation Tests Under Different Transformations (to test the robustness of the p-values of a given test (e.g.FlatLineTest()
,ReductiveHourglassTest()
,ReverseHourglassTest()
,EarlyConservationTest()
andLateConservationTest()
) to expression data transformations)New function
LateConservationTest()
: Perform Reductive Late Conservation Test (to test for a high-mid-low (or high-high-low) TAI or TDI pattern)New function
lcScore()
: Compute the Hourglass Score for the LateConservationTestinternal
rcpp
functions are now using Eigen to automatically enable parallelization
New Features
PlotSignature()
updated to be able to perform theTestStatistic = "LateConservationTest"
.PlotSignature()
now prints p-value as a subtitle rather than viaggplot2::annotate()
.tf()
now has apseudocount
parameter, which is useful for performing logarithmic transformations when there are genes with 0 counts.tf()
now has anintergerise
parameter, which is needed when applyingvst
orrlog
transformations.tf()
updated documentation for performing rank transformation, which assigns ranks to the gene expression values within each stage, based on their relative positions compared to other values.Improvements to existing test functions (
ecScore()
,rhScore()
andreversehourglassScore()
) to give a message when the phylotranscriptomic pattern is unlikely to follow the test statistics.FlatLineTest()
- newly returns the ks test statistics for the fitting of gammaFlatLineTest()
- improved fittingFlatLineTest()
- cpp functions are newly parallelized and progress bar is implemented for the computation of permutations
Bug and Issue Fixes
- Some changes to remove errors and warnings from
devtools::test()
anddevtools::check()
, when building this package, which has been accumulated from previous updates.
myTAI 1.0.0
New Functions
- New function
TEI()
: Compute the Transcriptome Evolutionary Index - New function
pMatrixTEI
: Compute Partial Transcriptome Evolutionary Index (TEI) Values - New function
pStrataTEI
: Compute Partial Transcriptome Evolutionary Index (TEI) Strata Values - New function
bootTEI
: Compute a Permutation Matrix of Transcriptome Evolutionary Index (TEI) - new internal
rcpp
functions to support parallel C++ computations forTEI()
,pMatrixTEI()
,pStrataTEI()
,bootTEI()
New Features
-
CollapseReplicates()
now returnstibble
objects -
PlotCategoryExpr()
received a new argumenty.ticks
myTAI 0.9.3
CRAN release: 2021-02-24
- removing the depreciated
std::random_shuffle()
function to sampleplylostratum
ordivergence stratum
columns and replacing it withstd::shuffle()
. See full discussion here. - removing depreciated function calls such as
dplyr::funs()
andtibble::is.tibble()
- updated unit tests
myTAI 0.9.1
CRAN release: 2019-03-10
- fixing a unit test that uses
set.seed(123)
which causes an error in the new R version3.6.0
due to the switch from anon-uniform "Rounding" sampler
to a"Rejection" sampler
in the new R version; the corresponding unit testtest-PlotEnrichment.R
was adjusted accordingly. Here the CRAN statement:
Note that this ensures using the (old) non-uniform “Rounding” sampler for all 3.x versions of R, and does not add an R version dependency. Note also that the new “Rejection” sampler which R will use from 3.6.0 onwards by default is definitely preferable over the old one, so that the above should really only be used as a temporary measure for reproduction of the previous behavior (and the run time tests relying on it).
myTAI 0.9.0
CRAN release: 2019-02-06
New Functions
new function
ReverseHourglassTest()
to perform aReverse Hourglass Test
. The Reverse Hourglass Test aims to statistically evaluate the existence of a reverse hourglass pattern based on TAI or TDI computations. The corresponding p-value quantifies the probability that a given TAI or TDI pattern (or any phylotranscriptomics pattern) does follow an hourglass like shape. A p-value < 0.05 indicates that the corresponding phylotranscriptomics pattern does rather follow a reverse hourglass (low-high-low) shape.new function
reversehourglassScore()
for computing theReverse Hourglass Score
for theReverse Hourglass Test
Updated Functionality
- function
PlotSignature()
receives a newTestStatistic
(TestStatistic = "ReverseHourglassTest"
) to perform arevserse hourglass test
(= testing the significance of a low-high-low pattern)
myTAI 0.7.0
CRAN release: 2018-04-11
Updates
New Functions
- new function
PlotCIRatio()
to compute and visualize TAI/TDI etc patters using bootstrapping and confidence intervals (contributed by @ljljolinq1010)
myTAI 0.6.0
CRAN release: 2017-07-03
Updates
is.ExpressionSet()
now prints out more detailed error messages when ExpressionSet format is violatedadapt
PlotContribution()
to new version ofdplyr
wheresummarise_each()
is deprecated.
Error message occurring after new dplyr
release was:
- Failure:
PlotContribution()
works properly with DivergenceExpressionSet input… (@test-PlotContribution.R#16) PlotContribution(DivergenceExpressionSetExample, legendName = “DS”) produced messages.
summarise_each()
is deprecated. Use summarise_all()
, summarise_at()
or summarise_if()
instead. To map funs
over all variables, use summarise_all()
summarise_each()
is deprecated. Use summarise_all()
, summarise_at()
or summarise_if()
instead. To map funs
over all variables, use summarise_all()
Is now fixed.
myTAI 0.5.0
CRAN release: 2017-03-14
New Functions
new function
PlotSignature()
allows users to plot evolutionary signatures across transcriptomes (based on ggplot2 -> new main visualization function aiming to replace thePlotPattern()
function)new function
TPI()
allows users to compute the Transcriptome Polymorphism Index introduced byGossmann et al., 2015
.new function
PlotMedians()
allows users to compute and visualize the median expression of all age categoriesnew function
PlotVars()
allows users to compute and visualize the expression variance of all age categories
Updates
PlotContribution()
is now based on ggplot2 and loses base graphics argumentsnow R/RcppExports.R and src/rcpp_funcs.cpp are included in the package due to previous compilation problems (see also stackoverflow discussion)
MatchMap()
is now based ondplyr::inner_join()
to match age category table with a gene expression datasetPlotCorrelation()
has been extended and optimized for producing high publication quality plotsPlotMeans()
is now based on ggplot2 and lost all base graphics arguments.PlotRE()
is now based on ggplot2 and lost all base graphics arguments.
myTAI 0.4.0
CRAN release: 2016-05-04
New Functions
- a new function
PlotSelectedAgeDistr()
allowing unsers to visualize the PS or DS gene distribution of a subset of genes stored in the input ExpressionSet object - a new function
PlotGroupDiffs()
allowing users to plot the significant differences between gene expression distributions of PS or DS groups - a new function
GroupDiffs()
allowing users to perform statistical tests to quantify the gene expression level differences between all genes of defined PS or DS groups
Updates
PlotDistribution()
now uses ggplot2 to visualize the PS or DS distribution and is also based on the new functionPlotSelectedAgeDistr()
; furthermore it loses argumentsplotText
and...
and gains a new argumentlegendName
remove arguments ‘main.text’ and ‘…’ from
PlotCorrelation()
PlotCorrelation()
is now based on ggplot2PlotGroupDiffs()
receives a new argumentgene.set
allowing users to statistically quantify the group specific PS/DS differences of a selected set of genesanalogously to
PlotGroupDiffs()
the functionGroupDiffs()
also receives a new argumentgene.set
allowing users to statistically quantify the group specific PS/DS differences of a selected set of genesFixing wrong x-axis labeling in
PlotCategoryExpr()
whentype = "stage-centered"
is specifiedPlotCategoryExpr()
now also prints out the PS/DS absolute frequency distribution of the selectedgene.set
myTAI 0.3.0
CRAN release: 2015-07-31
Vignettes
- adding examples for
PlotCategoryExpr()
toAdvanced
Vignette - adding examples for
PlotReplicateQuality()
toExpression
vignette
New Functions
- a new function
PlotCategoryExpr()
allowing users to plot the expression levels of each age or divergence category as boxplot, dot plot or violin plot - a new function
PlotReplicateQuality()
allowing users to visualize the quality of biological replicates
myTAI 0.2.1
CRAN release: 2015-07-23
Vignettes
- fixed a wrong example in the Enrichment vignette (https://github.com/HajkD/myTAI/commit/8d52fd60c274361dc9028dec3409abf60a738d8a)
Updates
-
PlotGeneSet()
andSelectGeneSet()
now have a new argumentuse.only.map
specifying whether or not instead of using a standardExpressionSet
aPhylostratigraphic Map
orDivergene Map
is passed to the function. - a wrong version of the edgeR Bioconductor package was imported causing version 0.2.0 to fail R CMD Check on unix based systems
myTAI 0.2.0
CRAN release: 2015-07-10
Vignettes
adding new vignette Taxonomy providing spep by step instructions on retrieving taxonomic information for any organism of interest
adding new vignette Expression Analysis providing use cases to perform gene expression data analysis with
myTAI
adding new vignette Enrichment providing step-by-step instructions on how to perform PS and DS enrichment analyses with
PlotEnrichment()
adding examples for
pStrata()
,pMatrix()
,pTAI()
,pTDI()
, andPlotContribution()
to the Introduction Vignette
New Functions
a new function
taxonomy()
allows users to retrieve taxonomic information for any organism of interest; this function has been taken from the biomartr package and was removed frombiomartr
afterwards. Please notice, that in myTAI version 0.1.0 the Introduction vignette referenced to thetaxonomy()
function inbiomartr
. This is no longer the case (since myTAI version 0.2.0), because nowtaxonomy()
is implemented in myTAI.the new
taxonomy()
function is based on the powerful R package taxize.a new function
SelectGeneSet()
allows users to fastly select a subset of genes in an ExpressionSeta new function
DiffGenes()
allows users to perform differential gene expression analysis with ExpressionSet objectsa new function
EnrichmentTest()
allows users to perform a Fisher’s exact test based enrichment analysis of over or underrepresented Phylostrata or Divergence Strata within a given gene set without having to plot the resulta new function
PlotGeneSet()
allows users to visualize the expression profiles of a given gene seta new function
PlotEnrichment()
allows users to visualize the Phylostratum or Divergence Stratum enrichment of a given Gene Set as well as computing Fisher’s exact test to quantify the statistical significance of enrichmenta new function
PlotContribution()
allows users to visualize the Phylostratum or Divergence Stratum contribution to the global TAI/TDI patterna new function
pTAI()
allows users to compute the phylostratum contribution to the global TAI patterna new function
pTDI()
allows users to compute the divergence stratum contribution to the global TDI pattern
Updates
-
FilterRNASeqCT()
has been renamed toExpressed()
allowing users to apply this filter function to RNA-Seq data as well as to microarray data -
PlotRE()
andPlotMeans()
are now based on colors from the RColorBrewer package (default) -
PlotRE()
andPlotMeans()
now have a new argumentcolors
allowing unsers to choose custom colors for the visualized relative or mean expression profiles -
geom.mean()
andharm.mean()
now are external functions accessible to themyTAI
user
myTAI 0.1.0
CRAN release: 2015-05-24
New Functions
a new function
pStrata()
allows users to compute partial TAI/TDI values for all Phylostrata or Divergence Strataa new function
CollapseReplicates()
allows users to combine replicate expression levels in ExpressionSet objectsa new function
FilterRNASeqCT()
allows users to filter expression levels ofExpressionSet
objects deriving from RNA-Seq count tables
Updates
function
MatchMap()
now receives a new argumentremove.duplicates
allowing users to delete duplicate gene ids (that might be stored in the input PhyoMap or DivergenceMap) during the process of matching a Map with an ExpressionSetFlatLineTest()
,ReductiveHourglassTest()
,EarlyConservationTest()
, andPlotPattern()
implement a new argumentcustom.perm.matrix
allowing users to pass their own (custom) permutation matrix to the corresponding function. All subsequent test statistics and p-value/std.dev computations are then based on this custom permutation matrixEarlyConservationTest()
andReductiveHourglassTest()
now have a new parametergof.warning
allowing users to choose whether or not non significant goodness of fit results should be printed as warningnow when specifying
TestStatistic = NULL
inPlotPattern()
only the TAI/TDI profile is drawn (without performing any test statistics); this is equavalent to performing:plot(TAI(PhyloExpressionSetExample)
function
combinatorialSignificance()
is now namedCombinatorialSignificance()
changing the title and description of the
myTAI
packagesome minor changes in vignettes and within the documentation of functions
myTAI 0.0.2
CRAN release: 2014-12-27
New Features in v. 0.0.2
combinatorialSignificance()
,FlatLineTest()
,ReductiveHourglassTest()
, andEarlyConservationTest()
now support multicore processingMatchMap()
has been entirely rewritten and is now based on dplyr; additionally it now has a new argumentaccumulate
that allows you to accumulate multiple expression levels to a unique expressiion level for a unique gene id
Vignettes
All three Vignettes: Introduction
, Intermediate
, and Advanced
have been updated and extended.
Bug Fixes
two small bugs in
ReductiveHourglassTest()
andEarlyConservationTest()
have been fixed that caused that instead of displaying 3 or 4 plots (par(mfrow=c(1,3))
orpar(mfrow=c(2,2))
) only 1 plot has been generateda small bug in
PlotMeans()
that caused the visualization of a wrong y-axis label when plotting only one group of Phylostrata or Divergence Strata