bagDeviations: bagDeviations

In caleblareau/chromVARxx: Augmented functionality for analysis of epigenomic variance

Description

Given a deviations object from the cisBP curtailed chromVARmotifs list, "bag" them according to correlation where the most variable goes first. Make sure to specify organism and correlation. The lower the the correlation, the less bagging that occurs. Row data then contains a comma-separated list of motifs that are bagged.

Usage

bagDeviations(object, cor, organism)

## S4 method for signature 'chromVARDeviations,numeric,character'
bagDeviations(object,
  cor = 0.7, organism = "human")

Arguments

object	chromVARDeviations object from chromVAR after
cor	= 0.7 minimum correlation between PWMS
organism	= "human"; only other option is "mouse"

Methods (by class)

• object = chromVARDeviations,cor = numeric,organism = character:

Author(s)

Caleb Lareau

Examples

rdsA<-paste0(system.file('rds',package='chromVARxx'),'/dev_humanSimple.rds')
object <- readRDS(rdsA)
bagged <- bagDeviations(object, cor = 0.3, organism = "human")

caleblareau/chromVARxx documentation built on May 14, 2019, 11:15 a.m.