Documentation issues about scde HOT 5 OPEN

Addressed issues above. Additional issues to address:

• At least 80% of man pages documenting exported objects
  must have runnable examples.The following pages do not:
  bwpca.Rd, knn.error.models.Rd, make.pagoda.app.Rd,
  pagoda.cluster.cells.Rd, pagoda.effective.cells.Rd,
  pagoda.gene.clusters.Rd, pagoda.pathway.wPCA.Rd,
  pagoda.reduce.loading.redundancy.Rd, pagoda.reduce.redundancy.Rd,
  pagoda.show.pathways.Rd, pagoda.subtract.aspect.Rd,
  pagoda.top.aspects.Rd, pagoda.varnorm.Rd, pagoda.view.aspects.Rd,
  scde.browse.diffexp.Rd, scde.error.models.Rd,
  scde.expression.difference.Rd, scde.expression.magnitude.Rd,
  scde.expression.prior.Rd, scde.failure.probability.Rd,
  scde.fit.models.to.reference.Rd, scde.posteriors.Rd,
  scde.test.gene.expression.difference.Rd, show.app.Rd,
  winsorize.matrix.Rd
  --> Basically...make examples for everything
• checking dependencies in R code ... WARNING
  '::' or ':::' import not declared from: ‘flashClust’
  'library' or 'require' calls not declared from:
  ‘Rook’ ‘extRemes’ ‘rjson’
  'library' or 'require' calls in package code:
  ‘Rook’ ‘extRemes’ ‘rjson’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
  ':::' call which should be '::': ‘mgcv:::s’
  See the note in ?::: about the use of this operator.
• checking Rd cross-references ... WARNING
  Missing link or links in documentation object 'pagoda.view.aspects.Rd':
  ‘view.aspects’
  --> Links missing for basically all other documentation

from scde.

Addressed issues above. Additional issues to address:

• checking dependencies in R code ... WARNING
  'library' or 'require' calls not declared from:
  ‘Rook’ ‘extRemes’ ‘rjson’
  'library' or 'require' calls in package code:
  ‘Rook’ ‘extRemes’ ‘rjson’
  Please use :: or requireNamespace() instead.

Vignettes still take forever to generate...save intermediates?

Examples with CPU or elapsed time > 5s
                                user system elapsed
scde.fit.models.to.reference 231.282 13.892 210.328
pagoda.subtract.aspect        57.929  0.802  61.327
pagoda.varnorm                55.790  0.692  58.479
scde.posteriors               31.474  0.360  32.723

from scde.

In the docs for ?scde.expression.difference I see:

ce conservative estimate of expression-fold change

I believe this should say "log2 fold-change".

Also, it should note that a positive fold-change means the expression is greater in the first level for a factor with two levels. (Here's a related Google Forums question.)

I'll try to make a pull request with these changes soon.

from scde.

• Tutorials need to have library("scde") added.
• Add http://pklab.med.harvard.edu/scde/pagoda.links.html link to let people browse sample results

from scde.

• See Jen's recommendation
• Use vertical bar or regex to choose multiple genes

from scde.