pride-r / prider Goto Github PK
View Code? Open in Web Editor NEWEMBL-EBI PRIDE Archive R package
Home Page: http://pride-r.github.io/prideR
EMBL-EBI PRIDE Archive R package
Home Page: http://pride-r.github.io/prideR
This class is for example needed when retrieving proteins for a given project. A class is needed that wraps functionality such as basic plots (with protein accession counts) and to get data as a data frame.
Similar to Project one
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get.list.ProjectSummary() Without parameters it should download all projects.
The PRIDE Archive projectSummary endpoint allows filtering results by different criteria. Provide this functionality in prideR.
projects <- get.list.ProjectSummary(count = 20)
projectsdata <- list.to.data.frame(projects)
Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
Error during wrapup: evaluation nested too deeply: infinite recursion / options(expressions=)?
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Create a class that represents lists of ProjectSummary instances and allow at least:
This class will provide interface for functions such as get.list.ProjectSummary, search, etc
add some demo about the package
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Add validity method for all classes, also try to add unit tests as well
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This needs to be done asap
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Restructure the classes according to Bioconductor's guideline
As a user it would be great to have a general statistics (number of proteins, projects and psms) by Instrument
Run R CMD check and fix all the warnings and errors
Enable users to type '?prideR' to view the document about the package
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