In CharlesJB/ProfilesMetagene: Demo of creation of genomic profiles with metagene

Demo: how to extract genomic profiles wiht metagene

0. Introduction

In this demo, we will see how it is possible to use metagene to extract the genomic profiles from bam files.

1. Preparing the files

We will work with the following bam files:

bam_files <- c(system.file("extdata/H3K4me1.bam", package = "ProfilesMetagene"),
               system.file("extdata/H3K27ac.bam", package = "ProfilesMetagene"))

We will use the following regions:

regions <- system.file("extdata/tidy_enhancers.txt", package = "ProfilesMetagene")
regions <- read.table(regions, header = TRUE)
regions <- makeGRangesFromDataFrame(regions, start.field = "chromStart",
               end.field = "chromEnd")
width(regions) <- 1000

We also need to make sure the seqlevels of the regions match the seqlevels of the bam files:

seqlevels(regions, force = TRUE) <- seqlevels(Rsamtools::BamFile(bam_files[1]))

2. Launching the metagene analysis

suppressMessages(library(metagene))
mg <- metagene$new(regions = regions, bam_files = bam_files, cores = 2)

3. Extracting the profiles

profiles <- mg$coverages

CharlesJB/ProfilesMetagene documentation built on May 6, 2019, 9:58 a.m.