pathSelect: Select pathways of interest for pathway-level resemblance...
In matianzhou/CAMO: Perform congruent analysis among model organisms

Description Usage Arguments Value Examples

Select pathways of interest The pathSelect is function to select pathways of interest for pathway-level resemblance analysis

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pathSelect(mcmc.merge.list, pathway.list, pathwaysize.lower.cut = 10,
  pathwaysize.upper.cut = 200, overlapsize.cut = 10, med.de.cut = 5,
  qfisher.cut = 0.01)

`mcmc.merge.list:`	a list of merged MCMC output matrices.
`pathway.list:`	list of pathway database.
`pathwaysize.lower.cut:`	pathway size lower bound cutoff;
`pathwaysize.upper.cut:`	pathway size upper bound cutoff;
`overlapsize.cut:`	lower bound cutoff of overlap size between genes from input data and genes from a pathway.
`med.de.cut:`	lower bound cutoff of median number of DE genes in a pathway.
`qfisher.cut:`	fisher q-value cutoff from the meta enrichment analysis.

an vector of selected pathway names.

## Not run: 
#mcmc.merge.list from the merge step
data(pathwayDB) ## include pathway.list
select.pathway <- pathSelect(mcmc.merge.list,pathway.list)
select.pathway.list <- pathway.list[select.pathway]

## End(Not run)