HarvardX PH525.5x Introduction to Bioconductor

Setup and GRange check

library(devtools)
install_github("genomicsclass/ERBS")
library(BiocInstaller)
biocVersion()

Setup GenomicRagnes

source("http://bioconductor.org/biocLite.R")
biocLite("GenomicRanges")

What is the class of HepG2 ? - GRanges

library(ERBS)
data(HepG2)
class(HepG2)
attributes(class(HepG2))

> class(HepG2)
[1] "GRanges"
attr(,"package")
[1] "GenomicRanges"

Counting regions. Explore the HepG2 object. How many regions are represented? - 303

HepG2
length(HepG2)
unique(HepG2@ranges)

> length(HepG2)
[1] 303

In what chromosome is the region with the highest signalValue? - chrx

> i = which.max(mcols(HepG2)$signalValue)
> i
[1] 120
> seqnames(HepG2[i])
factor-Rle of length 1 with 1 run
  Lengths:    1
  Values : chrX
Levels(93): chr1 chr2 chr3 ... chrUn_gl000248 chrUn_gl000249

(ref)[https://github.com/mbh038/PH525/blob/master/5x/Week%203%20Computing%20on%20Genomic%20Regions/Computing%20on%20Genomic%20Regions.rmd]