multi_ACS_ADS_global: Genome-wide congruence analysis for multiple pairs

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

Genome-wide congruence analysis for multiple pairs

Description

The multi_ACS_ADS_global is function to perform congruence analysis for multiple study pairs, generating genome-wide c-scores, d-scores and their permuted p-values.

Usage

multi_ACS_ADS_global(
  mcmc.merge.list,
  dataset.names,
  measure = "Fmeasure",
  B = 100
)

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.

Value

Four lists:

• ACS: genome-wide c-scores.

• ACSpvalue: p-values for genome-wide c-scores.

• ADS: genome-wide d-scores.

• ADSpvalue: p-values for genome-wide d-scores.

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

Examples

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

## End(Not run)

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