diffloop (version 1.0.2)

loopTest: Differential Loop Calling

Description

loopTest takes a loopfit object from the loopFit function and creates a loops object with additional columns in the rowData

Usage

loopTest(y, coef = 2, contrast, method = "QLF")
## S3 method for class 'loopfit,missing,missing,missing':
loopTest(y, coef = 2, contrast,
  method = "QLF")
## S3 method for class 'loopfit,numeric,missing,missing':
loopTest(y, coef = 2, contrast,
  method = "QLF")
## S3 method for class 'loopfit,missing,numeric,missing':
loopTest(y, coef = 2, contrast,
  method = "QLF")

Arguments

y

A loopfit object for association

coef

Specifies coefficient of design matrix

contrast

Specifies comparison of groups from design matrix

method

Specifies association method; only QLF is currently supported

Value

• A loops object with additional columns in rowData

Details

This function returns a loops object, which contains the results from an association in the rowData slot. The default association is using coefficient 2 from the model matrix (e.g. good for pair comparisons) but the user may specify a different coefficient. Currently, 'QLF' is the only supported method, but new features may be added in later developments. Users may also specify the contrast between the columns in the design matrix as used in edgeR.

Examples

# Differential loop fit
rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
jpn_loopfit <- loopFit(loops.small)
# Differential loop calling between naive and jurkat
assoc_jn <- loopTest(jpn_loopfit, coef = 2)