Reference Manual Edits

[lxw391]

see below, function SubsetPathwayData needs an example

[gabrielodom]

This function, and getPathPCLs() need examples.

[gabrielodom]

After making the vignette edits, build the PDF. @lxw391, please mark any functions you find without examples in this thread.

[gabrielodom]

Updated the examples in getAssay(), getPathwayCollection(), SubsetPathwayData(), getResponse(), getEvent(), getEventTime(), getPathPCLs(), and AESPCA_pVals().

[gabrielodom]

Updated the example in LoadOntoPCs().

[lxw391]

@gabrielodom Could you tell me where are the pdf file for the reference manual is located? Thanks.

[gabrielodom]

I've rebuilt the help manual. I'll share the pdf on dropbox in the top level of Ban and Odom -Bioconductor package/.

Also, I've changed the documentation level of many of the internal functions to "internal" (through the @keywords tag). These functions will be excluded from the manual. If you'd like any of these functions to be included, just ask, and I'll remove the tag.

[gabrielodom]

Please leave any manual edit requests as comments here.

[gabrielodom]

Edits:

• the URLs on the first page should be reversed
• wrong quotes around User Guides
• change documentation names: i. getAssay --> SubsetOmicsPath ii. getEventTime --> SubsetOmicsSurv iii. getResponse --> SubsetOmicsResponse iv. [[.pathwayCollection --> SubsetPathwayCollection
• normalize should be internal
• Transpose Assay should ask if the names are in the first column

[gabrielodom]

Updated the documentation title of LoadOntoPCs().

[gabrielodom]

Closed accidentally in the merge.