rankFactorsbyDomain: Function to help selecting candidate epigenetic factors based...

In chroGPS: chroGPS2: Generation, visualization and differential analysis of epigenome maps

Description

Function to help selecting candidate epigenetic factors based on Epigenetic Domain cohesion/separation. This function ranks all combinations of a certain size of epigenetic factors in the selected domain based on how much they contribute to provide a good cohesion and separation of the points of their epigenetic domain against the rest. This allows selection of the 'best' combination of epigenetic factors in a certain domain to generate informative epigenetic maps.

Usage

rankFactorsbyDomain(d, sampleinfo, ranktype = "domainDist", selName = "Color", selValue, k = NULL, mc.cores = 1)

Arguments

d	A distGPS object with the epigenetic distances, see function distGPS.
sampleinfo	A data.frame object with at least the domain information for the epigenetic factors in the provided distance matrix. Sampleinfo rownames need to match row and colnames in the distance matrix.
ranktype	Character vector indicating the method to use. Currently only supporting 'domainDist' method.
selName	Name of the column containing the epigenetic domain information in the sampleinfo dataframe.
selValue	Character indicating the name of the domain to be evaluated.
k	Size of the factor combination to be evaluated.
mc.cores	Cores to use in calls to parallel::mclapply.

Value

Named list with each evaluated combination of factors and:

inter	Their resulting average inter-domain distance.
intra	Their resulting average intra-domain distance.

Author(s)

Oscar Reina.

See Also

distGPS, domainDist

Examples

## Rank Factors by Domain, using intra/inter domain distance

data(s2)
data(toydists)
#d <- distGPS(s2,metric='avgdist',mc.cores=8) # Compute distances
rownames(s2names) <- s2names$ExperimentName

# Known domains
# Call rankFactorsbyDomain for HP1a repression domain, select a combination of 4
# factors
library(caTools)
rank.factors.4 <- rankFactorsbyDomain(d,s2names,ranktype='domainDist',selName='Color',selValue='lightblue',k=3,mc.cores=1) # Test HP1a repression
ddd <- as.data.frame(do.call(rbind,lapply(rank.factors.4,unlist)))
ddd <- ddd[order(ddd$intra,decreasing=FALSE),]
head(ddd)

chroGPS documentation built on Oct. 31, 2019, 4:52 a.m.