importFromRawMode: Imports PEPs created in raw mode

In franapoli/gep2pep: Creation and Analysis of Pathway Expression Profiles (PEPs)

Description

Raw mode is meant to deal with large collections of PEPs (like hundreds of thousands). In this case, problems may arise while trying to convert GEPs by loading all of them in memory at once. Raw mode is meant to be used with HDF5 format, which allows to load subsets of GEPs from the disk. buildPEPs, when used in raw mode, can create the corresponding subsets of PEPs, so that the job can be distributed on a computer cluster. importFromRawMode is meant to join the chunks into HDF5 matrices, which are than stored into the repository. The .loadPEPs function can seamlessly load PEPs stored in normal (RDS) or HDF5 format.

Usage

importFromRawMode(rp, path = file.path(rp$root(), "raw"),
  collections = "all")

Arguments

rp	A repository created by createRepository.
path	Path were raw PEPs are stored (default is a "raw" directory under the repository root folder).
collections	A subset of the collection names returned by getCollections. If set to "all" (default), all the collections in rp will be used.

Details

PEPs are expect to be found at the specified path and follow the naming convention as generated by buildPEPs. According to such convention, each file is named usign the format category_subcategory#chunknumber.RDS. All non-alphanumeric characters from the original category and subcategory names are replace with an underscore (in rare cases this could create ambiguity that should be manually prevented). All chunks for the same subcategory are joined together following the chunk numbers into a single HDF5 matrix and stored in the repository as an "attachment" (see repo documentation).

Note that raw PEPs (by default everything at repository_root/raw) can be safly removed once they have been imported.

Value

Nothing, used for side effects.

See Also

buildPEPs

Examples

db <- loadSamplePWS()
repo_path <- file.path(tempdir(), "gep2pepTemp")

rp <- createRepository(repo_path, db)

## The following will create PEPs in 2 separate files
geps <- loadSampleGEP()
buildPEPs(rp, geps[,1:2], progress_bar=FALSE,
    rawmode_id=1)
buildPEPs(rp, geps[,3:5], progress_bar=FALSE,
    rawmode_id=2)

## The separate files are then merged into one (possibly big) file
## in HDF5 format

importFromRawMode(rp)

## Now most operations (excluding the addition of new PEPs to
## existing collections) will be available as usual.

unlink(repo_path, TRUE)

franapoli/gep2pep documentation built on May 30, 2019, 4:34 p.m.