In mikelove/alpineData: Data for the alpine package vignette

Exploring the GAlignmentPairs in alpineData

We first load the alpineData package:

library(alpineData)

This package contains the following four GAlignmentPairs objects. We can access these directly with named functions:

ERR188297()
ERR188088()
ERR188204()
ERR188317()

Or we can access them using the ExperimentHub interface:

eh <- ExperimentHub()
query(eh, "ERR188")
eh[["EH166"]]

For details on the source of these files, and on their construction see ?alpineData and the scripts:

• inst/scripts/make-metadata.R
• inst/scripts/make-data.Rmd

We can take a quick look at the paired alignments from one file. For example their distribution on the different chromosomes:

library(GenomicAlignments)
gap <- ERR188297()
barplot(sort(table(seqnames(gap))[1:25], decreasing=TRUE),
        las=3, main="Distribution of reads")

Histograms of read starts for the first read on chromosome 1:

gap1 <- gap[seqnames(gap) == "1"]
starts <- start(first(gap1))
par(mfrow=c(2,2))
hist(starts,col="grey")

mikelove/alpineData documentation built on May 22, 2019, 10:52 p.m.