Fixes #66

Groups (and paths) were being simulted in alphanumeric rather than number
order. Fixed by making the Group column a factor.

Fixes #49

Fixes #64

Also remove lingering references to phenoData and featureData

Problem using factor to index matrix

* master:
  Fix group factors bug

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@131740 bc3139a8-67e5-0310-9ffc-ced21a209358

* master: (183 commits)
  Run checks
  Add batch effects to vignette
  Update splatEstimate to set batchCells
  Add batch effects to splatSimulate
  Update SplatParams
  Bump version number
  Update citation
  Fix error handling when fitting means
  Fix comparison plots
  Bioconductor 3.5 release
  bump x.y.z versions to odd y after creation of 3_5 branch
  Creating branch for BioC 3.5 release
  bump x.y.z versions to even y prior to creation of 3_5 branch
  Update NEWS and DESCRIPTION
  Version 0.99.15
  Remove dropout.present estimation
  Add limits to zeros plots
  Adjust default splat DE fac params
  Add BPPARAM to scDDSimulate
  Add summariseDiff function
  ...

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@131029 bc3139a8-67e5-0310-9ffc-ced21a209358

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/splatter@129128 bc3139a8-67e5-0310-9ffc-ced21a209358

* master:
  Version 0.99.12
  Run checks
  Warn if bcv.df is infinite
  Update addFeatureStats col names
  Update progress message
  Switch to boxplots in compareSCESets
  Change Lun2 nGenes estimate
  Add diffSCESets to vignette
  Add diffSCESets function

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127605 bc3139a8-67e5-0310-9ffc-ced21a209358

* master:
  Version 0.99.12
  Run checks
  Warn if bcv.df is infinite
  Update addFeatureStats col names
  Update progress message
  Switch to boxplots in compareSCESets
  Change Lun2 nGenes estimate
  Add diffSCESets to vignette
  Add diffSCESets function

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127605 bc3139a8-67e5-0310-9ffc-ced21a209358

* master:
  Version 0.99.11
  Run checks
  Fix mean-zeros scale
  Make lun2Estimate parallel
  Allow non-interger Lun 2 lib sizes
  Fix dropout eta

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127511 bc3139a8-67e5-0310-9ffc-ced21a209358

* master:
  Version 0.99.11
  Run checks
  Fix mean-zeros scale
  Make lun2Estimate parallel
  Allow non-interger Lun 2 lib sizes
  Fix dropout eta

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127511 bc3139a8-67e5-0310-9ffc-ced21a209358

Remove cell component

* master:
  Version 0.99.10
  Remove out.loProb from vignette
  Update default Splat parameters
  Remove out.loProb parameter
  Update estimation procedure

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127213 bc3139a8-67e5-0310-9ffc-ced21a209358

* master:
  Version 0.99.10
  Remove out.loProb from vignette
  Update default Splat parameters
  Remove out.loProb parameter
  Update estimation procedure

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127213 bc3139a8-67e5-0310-9ffc-ced21a209358

Decided it was unnecessary

* master: (123 commits)
  Fix non-linear path factors
  Bump verison number
  Set some examples to not run to save check time
  Initalise scDatEx to avoid NOTE
  Tidy up and bump version
  Replace 1:x
  Remove splatter.Rproj
  Add more detail about counts matrix
  Add installation to vignette
  Set R_TESTS environment
  Bump version to start build
  splatter 0.99.3
  Updata scDDEstimate
  Add condition parameter
  Modify SCDDParams to take SummarizedExperiment
  Add logo to vignettes directory
  Remove scDD github remote
  Update to R-devel
  Address Bioconductor build warnings, notes
  Prepare for Bioconductor submission
  ...

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@126081 bc3139a8-67e5-0310-9ffc-ced21a209358

* master: (123 commits)
  Fix non-linear path factors
  Bump verison number
  Set some examples to not run to save check time
  Initalise scDatEx to avoid NOTE
  Tidy up and bump version
  Replace 1:x
  Remove splatter.Rproj
  Add more detail about counts matrix
  Add installation to vignette
  Set R_TESTS environment
  Bump version to start build
  splatter 0.99.3
  Updata scDDEstimate
  Add condition parameter
  Modify SCDDParams to take SummarizedExperiment
  Add logo to vignettes directory
  Remove scDD github remote
  Update to R-devel
  Address Bioconductor build warnings, notes
  Prepare for Bioconductor submission
  ...

From: Luke Zappia <lazappi@users.noreply.github.com>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@126081 bc3139a8-67e5-0310-9ffc-ced21a209358

Fix bug that meant non-linear path factors weren't stored in output of
splatSimulatePaths

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@125902 bc3139a8-67e5-0310-9ffc-ced21a209358

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@125902 bc3139a8-67e5-0310-9ffc-ced21a209358

* Bump R version to 3.4
* Add row, col names to matrices