BSdataSet-class: Class "BSdataSet"

In methylPipe: Base resolution DNA methylation data analysis

Description

This class is used in the methylPipe library to store a set of BSdata objects

Objects from the Class

Objects can be created by calls of the form new("BSdataSet", ...) or using the function BSdataSet(org,Objlist,names), see below.

Slots

Objlist:

Object of class "list" : a list with more than one item, where each item is a BSdata object

names:

Object of class "character" : vector of the names of the objects, i.e. the sample names

group:

Object of class "character" : indicating conditions and replicates; replicated samples within the same condition have to be assigned the same group name; if object has only two groups, "C"(control) and "E" (Experiment) should be specified as groups name

org:

refrence genome of class BSgenome

Methods

"[["

signature(x = "BSdataSet"): subsets the BSdataSet returning a specific BSdata object

"[[<-"

signature(x = "BSdataSet"): replaces the specific BSdata object in the BSdataSet

"["

signature(x = "BSdataSet"): subsets the BSdataSet returning another BSdataSet

Author(s)

Mattia Pelizzola, Kamal Kishore

See Also

BSdata-class,findDMR

Examples

require(BSgenome.Hsapiens.UCSC.hg18)
uncov_GR <- GRanges(Rle('chr20'), IRanges(c(14350,69251,84185), c(18349,73250,88184)))
H1data <- system.file('extdata', 'H1_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
H1.db <- BSdata(file=H1data, uncov=uncov_GR, org=Hsapiens)
IMR90data <- system.file('extdata', 'IMR90_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
IMR90.db <- BSdata(file=IMR90data, uncov=uncov_GR, org=Hsapiens)
H1.IMR90.set <- BSdataSet(org=Hsapiens, group=c("C","E"), IMR90=IMR90.db, H1=H1.db)

methylPipe documentation built on Nov. 8, 2020, 6:51 p.m.