Documentation issues

[JEFworks]

Undocumented code objects: ‘make.pagoda.app’ ‘o.ifm’ ‘pagoda.reduce.redundancy’ ‘pagoda.view.aspects’ ‘scde.edff’

Undocumented data sets: ‘o.ifm’ ‘scde.edff’

Undocumented arguments in documentation object 'pagoda.cluster.cells' ‘verbose’ ‘return.details’

Undocumented arguments in documentation object 'pagoda.reduce.loading.redundancy' ‘abs’

Documented arguments not in \usage in documentation object 'pagoda.show.pathways': ‘show.Colv’

Undocumented arguments in documentation object 'scde.browse.diffexp' ‘port’

Undocumented arguments in documentation object 'scde.error.models' ‘linear.fit’ ‘local.theta.fit’ ‘theta.fit.range’

Undocumented arguments in documentation object 'scde.posteriors' ‘ensemble.posterior’

Argument items with no description in Rd object 'pagoda.show.pathways': ‘...’

[JEFworks]

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

[JEFworks]

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

[slowkow]

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.

[JEFworks]

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

[JEFworks]

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