loopAssoc: Generalized differential Loop Calling

Description Usage Arguments Details Value Examples

Description

loopAssoc takes a loops object and prepares it for the returns another loops object with summary statistics per-loop in the rowData

Usage

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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)

Arguments

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

Details

By the default, we generate is to generate a design matrix from [email protected]$groups. Currently, 'edgeR' and 'Voom' are the two supported association methods, but new association tests may be added in later developments.

Value

A loops object

Examples

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# Differential loop fit
rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
# assoc <- loopAssoc(loops.small, coef = 2)

Bioconductor-mirror/diffloop documentation built on June 1, 2017, 7:35 a.m.