mergeMCMC: Merge multiple MCMCout datasets preparing for cross-species...

In matianzhou/CAMO: Perform congruent analysis among model organisms

Description

Merge multiple MCMCout datasets The mergeMCMC is function to merge multiple MCMCout datasets by matching orthologs

Usage

mergeMCMC(mcmc.list, species, ortholog.db, ortholog.file = NULL,
  reference = 1)

Arguments

mcmc.list:	a list of MCMC output matrices.
species:	a vector specie names of same length as mcmc.list.
ortholog.db:	the ortholog object (in R environment)
ortholog.file:	the ortholog file to be imported
reference:	the index of the reference data, the outputted merged list will be named using the rownames of this data.

Value

an merged list of multiple MCMCout datasets (with same number of rows and rownames)

Examples

## Not run: 
data(hb)
summaryDE <- indDE(data=data,group=as.factor(group),data.type="microarray",
                  case.label="2", ctrl.label="1")
hb_pData <- summaryDE[,c(3,1)]
hb_MCMCout <- bayes(hb_pData, seed=12345)
data(hs)
summaryDE <- indDE(data=data,group=as.factor(group),data.type="microarray",
                  case.label="2", ctrl.label="1")
hs_pData <- summaryDE[,c(3,1)]
hs_MCMCout <- bayes(hs_pData, seed=12345)
data(ht)
summaryDE <- indDE(data=data,group=as.factor(group),data.type="microarray",
                  case.label="2", ctrl.label="1")
ht_pData <- summaryDE[,c(3,1)]
ht_MCMCout <- bayes(ht_pData, seed=12345)
data(mb)
summaryDE <- indDE(data=data,group=as.factor(group),data.type="microarray",
                  case.label="2", ctrl.label="1")
mb_pData <- summaryDE[,c(3,1)]
mb_MCMCout <- bayes(mb_pData, seed=12345)
data(ms)
summaryDE <- indDE(data=data,group=as.factor(group),data.type="microarray",
                  case.label="2", ctrl.label="1")
ms_pData <- summaryDE[,c(3,1)]
ms_MCMCout <- bayes(ms_pData, seed=12345)
data(mt)
summaryDE <- indDE(data=data,group=as.factor(group),data.type="microarray",
                  case.label="2", ctrl.label="1")
mt_pData <- summaryDE[,c(3,1)]
mt_MCMCout <- bayes(mt_pData, seed=12345)

#1. single pair example
mcmc.list <- list(hb_MCMCout,mb_MCMCout)
species <- c("human","mouse")
data(hm_orth)
mcmc.merge.list <- mergeMCMC(mcmc.list,species = species,
ortholog.db = hm_orth, reference=1) 

#2. multiple pairs example
mcmc.list <- list(hb_MCMCout,hs_MCMCout,ht_MCMCout,
                  mb_MCMCout,ms_MCMCout,mt_MCMCout)
species <- c(rep("human",3), rep("mouse",3))
data(hm_orth)
mcmc.merge.list <- mergeMCMC(mcmc.list,species = species,
ortholog.db = hm_orth, reference=1)                

## End(Not run)

matianzhou/CAMO documentation built on May 21, 2019, 10:12 a.m.