domainDist: Overview of intra and inter-domain distances.

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

Description

Given a distance of pairwise distances or dissimilarities between elements, return intra and inter-group sets of distances based on a given group definition. This is useful to get an insight on domain robustness for functional related genes or factors.

Usage

domainDist(d, gps='factors', domain, type='intra', col='white', avg=FALSE,
plot=TRUE, ...)

Arguments

d	Distance/Dissimilarities matrix, usually the slot d on a distGPS object, but any distance matrix can be given as input.
gps	'factors' for a chroGPS-factors distance matrix, 'genes' for a chroGPS-genes one.
domain	Character vector with group identity for each element d. It can be a functional domain classification (i.e. 'Activation', 'Repression', etc), given for each factor on a chroGPS-factors map or for each gene in a chroGPS-genes map. However, any classification of interest can be used (pathways, gene ontology, etc.)
type	Intradomain ('intra') or Interdomain ('inter') distance overview.
col	Character vector with colors to be passed to plot.
avg	TRUE to return also the average inter or intra domain distance.
plot	TRUE to generate inter/intra domain boxplots.
...	Additional parameters given to the generic function plot.

Value

List of inter or intra domain distances.

Examples

# Not run
# data(s2)
# d <- distGPS(s2,metric='avgdist',mc.cores=1)
# d.intra <- domainDist(as.matrix(d),domain=s2names$Color,type='intra',plot=TRUE)
# d.inter <- domainDist(as.matrix(d),domain=s2names$Color,type='inter',plot=TRUE)

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