summary-loops-method: Link the anchors and interactions back together

In aryeelab/diffloop: Identifying differential DNA loops from chromatin topology data

Description

summary takes a loops object and breaks the loop data structure resulting in a data.frame.

Usage

## S4 method for signature 'loops'
summary(object)

Arguments

object

A loops object to be summarized

Details

This function returns a data.frame where the left and right anchors are visualized together along with the loop width, individual counts, and any anchor meta-data that has been annotated into the anchors GRanges object as well as any rowData varianble. Finally, the region column contains the coordinates that readily facilitates visualization of loop in UCSC or DNAlandscapeR by padding the loop by 25kb on either side.

Value

A data.frame

Examples

# Summarizing the first ten loops in \code{loops.small}
rda<-paste(system.file('rda',package='diffloop'),'loops.small.rda',sep='/')
load(rda)
summarydf <- summary(loops.small[1:10,])
# Summarizing the loops and significance results between naive and primed
summarylt <- summary(quickAssoc(loops.small[,1:4])[1:10,])

aryeelab/diffloop documentation built on May 12, 2019, 3:42 a.m.