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Runs multilevel Monte-Carlo variant for performing gene sets co-regulation analysis using the RAMP_DB metabolite/gene database.

Source: R/PathwayAnalysis.R
RunRAMPgeseca.Rd

This function is adapted from the fgsea::geseca package to identify significantly expressed RAMP_DB pathways based on an expression/feature embedding matrix.

Usage

RunRAMPgeseca(
  E,
  minSize = 1,
  maxSize = nrow(E) - 1,
  center = TRUE,
  scale = FALSE,
  sampleSize = 101,
  eps = 1e-50,
  nproc = 0,
  BPPARAM = NULL,
  nPermSimple = 1000,
  database = NULL,
  database_version = "latest",
  database_source = c("auto", "bundled", "local"),
  database_local_dir = NULL
)

Arguments

E

expression matrix, rows corresponds to RAMP_IDs, columns corresponds to cell barcodes.

minSize

Minimal size of a gene set to test. All pathways below the threshold are excluded (default = 1).

maxSize

Maximal size of a gene set to test. All pathways above the threshold are excluded (default = nrow(E) - 1).

center

a logical value indicating whether the gene expression should be centered to have zero mean before the analysis takes place (default = TRUE).

scale

a logical value indicating whether the gene expression should be scaled to have unit variance before the analysis takes place (default = FALSE).

sampleSize

sample size for conditional sampling (default = 101).

eps

This parameter sets the boundary for calculating P-values (default = 1e-50).

nproc

If not equal to zero sets BPPARAM to use nproc workers (default = 0).

BPPARAM

Parallelization parameter used in bplapply (default = NULL).

nPermSimple

Number of permutations in the simple geseca implementation for preliminary estimation of P-values (default = 1000).

database

Optional named list of database resources, normally created by LoadSpaMTPDatabase().

database_version

Database snapshot version used for pathway lookup.

database_source

Database source; see LoadSpaMTPDatabase().

database_local_dir

Optional local RDS resource directory.

Value

A table with GESECA results. Each row corresponds to a tested RAMP_DB pathway.

Examples

utils::str(formals(RunRAMPgeseca))
#> Dotted pair list of 14
#>  $ E                 : symbol 
#>  $ minSize           : num 1
#>  $ maxSize           : language nrow(E) - 1
#>  $ center            : logi TRUE
#>  $ scale             : logi FALSE
#>  $ sampleSize        : num 101
#>  $ eps               : num 1e-50
#>  $ nproc             : num 0
#>  $ BPPARAM           : NULL
#>  $ nPermSimple       : num 1000
#>  $ database          : NULL
#>  $ database_version  : chr "latest"
#>  $ database_source   : language c("auto", "bundled", "local")
#>  $ database_local_dir: NULL
# E <- SpaMTP@reductions$pca.rev@feature.loadings
# sig_pathways <- RunRAMPgeseca(E, minSize=15, maxSize=500)