pathSelect: Select pathways of interest for pathway-level congruence...

In CAMO-R/Rpackage: Perform cross-species resemblance analysis

Select pathways of interest for pathway-level congruence analysis

Description

The pathSelect is function to select pathways of interest for pathway-level congruence analysis by meta pathway enrichement analysis.

Usage

pathSelect(
  mcmc.merge.list,
  pathway.list,
  pathwaysize.lower.cut = 10,
  pathwaysize.upper.cut = 200,
  overlapsize.cut = 10,
  med.de.cut = 5,
  min.de.cut = 0,
  qfisher.cut = 0.05,
  topPath.indStudy.num = NULL
)

Arguments

mcmc.merge.list:	a list of merged MCMC output matrices.
pathway.list:	list of pathway database. This can be any pathway list from external sources or selected from the contained pathway data in CAMO package.
pathwaysize.lower.cut:	pathway size lower bound cutoff;
pathwaysize.upper.cut:	pathway size upper bound cutoff;
overlapsize.cut:	the lower bound cutoff of overlap size between genes from input data and genes from a pathway.
med.de.cut:	the lower bound cutoff of minimum number of DE genes in a pathway.
qfisher.cut:	fisher q-value cutoff from the meta enrichment analysis.
topPath.indStudy.num:	if not NULL, only the union of top pathways is considered.

Value

a vector of selected pathway names.

Examples

## Not run: 
#mcmc.merge.list from the merge step (see the example in function 'merge')
data(human.pathway.list) ## include pathway.list
select.pathway = pathSelect(mcmc.merge.list,pathway.list,
                            pathwaysize.lower.cut = 5,
                            pathwaysize.upper.cut=200,
                            overlapsize.cut = 5, med.de.cut =3,
                            qfisher.cut = 0.05)
select.pathway.list = pathway.list[select.pathway]

## End(Not run)

CAMO-R/Rpackage documentation built on July 20, 2023, 6:04 a.m.