loopAssoc {diffloop} | R Documentation |
loopAssoc
takes a loops
object and prepares it for the
returns another loops
object with summary statistics
per-loop in the rowData
loopAssoc(y, method = "edgeR", design = NULL, coef = NULL, contrast = NULL) ## S4 method for signature 'loops' loopAssoc(y, method = "edgeR", design = NULL, coef = NULL, contrast = NULL)
y |
A loops object for association |
method |
Specifies association; either "Voom" or "edgeR" |
design |
A design matrix of the samples; required for "Voom" |
coef |
A vector for the coefficient of GLM. See edgeR manual |
contrast |
A vector for the contrast. See edgeR manual |
By the default, we generate is to generate a design matrix from
loops@colData$groups
. Currently, 'edgeR' and 'Voom' are the
two supported association
methods, but new association tests may be added in later developments.
A loops object
# Differential loop fit rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/') load(rda) # assoc <- loopAssoc(loops.small, coef = 2)