buildPEPs {gep2pep}R Documentation

Build PEPs from GEPs and stores them in the repository.

Description

Given a matrix of ranked lists of genes (GEPs) and a gep2pep repository, converts GEPs to PEPs and stores the latter in the repository.

Usage

buildPEPs(rp, geps, parallel = FALSE, collections = "all",
  replace_existing = FALSE, progress_bar = TRUE)

Arguments

rp

A repository created by createRepository.

geps

A matrix of ranks where each row corresponds to a gene and each column to a condition. Each column must include all ranks from 1 to the number of rows. Row and column names must be defined. Row names will be matched against gene identifiers in the pathways collections, and unrecognized gene names will not be used.

parallel

If TRUE, gene sets will be processed in parallel. Requires a parallel backend.

collections

A subset of the collection names returned by getCollections. If set to "all" (default), all the collections in rp will be used.

replace_existing

What to do if PEPs, identified by column names of geps are already present in the repository. If set to TRUE, they will be replaced, otherwise they will be skipped and only PEPs of new conditions will be computed and added. Either ways, will throw a warning.

progress_bar

If set to TRUE (default) will show a progress bar updated after coversion of each column of geps.

Value

Nothing. The computed PEPs will be available in the repository.

See Also

buildPEPs

Examples

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

rp <- createRepository(repo_path, db)
## Repo root created.
## Repo created.
## [15:45:06] Storing pathway data for collection: c3_TFT
## [15:45:06] Storing pathway data for collection: c3_MIR
## [15:45:06] Storing pathway data for collection: c4_CGN

rp
##          ID   Dims     Size
## c3_TFT_sets   10   18.16 kB
## c3_MIR_sets   10   17.25 kB
## c4_CGN_sets   10     6.9 kB

## Loading sample gene expression profiles
geps <- loadSampleGEP()

geps[1:3,1:3]
##       (+)_chelidonine (+)_isoprenaline (+/_)_catechin
## AKT3               88              117            417
## MED6              357              410             34
## NR2E3             383              121            453

buildPEPs(rp, geps)

rp
##           ID  Dims     Size
##   c3_TFT_sets   10 18.16 kB
##   c3_MIR_sets   10 17.25 kB
##   c4_CGN_sets   10   6.9 kB
##        c3_TFT    2  1.07 kB
##        c3_MIR    2  1.07 kB
##        c4_CGN    2  1.04 kB

unlink(repo_path, TRUE)


[Package gep2pep version 1.0.0 Index]