buildPEPs {gep2pep} | R Documentation |
Given a matrix of ranked lists of genes (GEPs) and a gep2pep
repository, converts GEPs to PEPs and stores the latter in the
repository.
buildPEPs(rp, geps, parallel = FALSE, collections = "all", replace_existing = FALSE, progress_bar = TRUE)
rp |
A repository created by |
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
|
replace_existing |
What to do if PEPs, identified by column
names of |
progress_bar |
If set to TRUE (default) will show a progress
bar updated after coversion of each column of |
Nothing. The computed PEPs will be available in the repository.
buildPEPs
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)