Runs multilevel Monte-Carlo variant for performing gene sets co-regulation analysis using the RAMP_DB metabolite/gene database.
Source:R/PathwayAnalysis.R
RunRAMPgeseca.RdThis 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
)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).