domainDist {chroGPS} | R Documentation |
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.
domainDist(d, gps='factors', domain, type='intra', col='white', avg=FALSE, plot=TRUE, ...)
d |
Distance/Dissimilarities matrix, usually the slot |
gps |
'factors' for a chroGPS-factors distance matrix, 'genes' for a chroGPS-genes one. |
domain |
Character vector with group identity for each element |
type |
Intradomain ('intra') or Interdomain ('inter') distance overview. |
col |
Character vector with colors to be passed to |
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 |
List of inter or intra domain distances.
# 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)