Fixes #82

Fixes #82

Tidy and improve examples

Tidy and improve examples

* master:
  Bump version number
  Run checks
  Patch fix to lun2Estimate from basics branch
  Update summariseDiff
  Add counts check to scDDEstimate
  Adjust nEE/nEP estimation
  Update scDD estimation

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@131258 bc3139a8-67e5-0310-9ffc-ced21a209358

Error when scran::computeSumFactors returns negative values

Error when scran::computeSumFactors returns negative values

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

* master:
  Version 0.99.13
  Run checks
  Update Lun2 documentation
  Modify Lun2Params to use data.frame

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127694 bc3139a8-67e5-0310-9ffc-ced21a209358

* master:
  Version 0.99.13
  Run checks
  Update Lun2 documentation
  Modify Lun2Params to use data.frame

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

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/splatter@127694 bc3139a8-67e5-0310-9ffc-ced21a209358

Store gene parameters in data.frame rather than separate vectors. Forces them
to be same length and allows more independence between gene parameters and
nGenes. Checking for differences between the number of gene parameters and
nGenes, and sampling if necessary, is now done in `lun2Simulate` rather than
`validObject`. The same is true for nCells and lib.sizes.

* 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

No gives the number of rows in the original counts

* 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

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

* Add locfit to NAMESPACE
* Add return values to logistic, showPP documentation
* Delete commented mergeParams function
* Switch to aes_string in compareSCESets
* Add examples to getParam, setParam
* Adjust line lengths
* Adjust indentation

Some parameters weren't being passed from SCESet method to matrix
method