multi_ACS_ADS_pathway: Pathway level congruence analysis for multiple pairs

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

Pathway level congruence analysis for multiple pairs

Description

The multi_ACS_ADS_pathway is function to perform congruence analysis for multiple pairs, generating pathway-specific c-scores, d-scores and their permuted p-value.

Usage

multi_ACS_ADS_pathway(
  mcmc.merge.list,
  dataset.names,
  select.pathway.list,
  measure = "Fmeasure",
  B = 100,
  parallel = F,
  n.cores = 4
)

Arguments

mcmc.merge.list:	a list of merged MCMC output matrices.
dataset.names:	a vector of dataset names.
measure:	three types of scores to be used: "youden", "Fmeasure","geo.mean". Default is "Fmeasure".
B:	number of permutations.
parallel:	whether to perform parallel ('mclapply' will be used if parallel=T) computing in permutation.
n.cores:	if parallel=T, the number of cores to use (mc.cores parameter in 'mclapply' function).

Value

Four lists:

• ACS.mat: pathway-specific c-scores.

• ACSpvalue.mat: p-values for pathway-specific c-scores.

• ADS.mat: pathway-specific d-scores.

• ADSpvalue.mat: p-values for pathway-specific d-scores.

In addition, the four data matrices are written to a folder named "ACS_ADS_Pathway".

Examples

## Not run: 
#mcmc.merge.list from the merge step (see the example in function 'merge')
#select.pathway.list from the pathSelect step (see the example in function 'pathSelect')
dataset.names = c("hb","hs","ht","ha","hi","hl",
                  "mb","ms","mt","ma","mi","ml")
ACS_ADS_pathway = multi_ACS_ADS_pathway(mcmc.merge.list,dataset.names,
                                        select.pathway.list,
                                        measure="Fmeasure",
                                        B=1000,parallel=F)

## End(Not run)

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