We first load the alpineData package:
library(alpineData)
## Loading required package: ExperimentHub
## Loading required package: BiocGenerics
## Loading required package: parallel
##
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:parallel':
##
## clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
## clusterExport, clusterMap, parApply, parCapply, parLapply,
## parLapplyLB, parRapply, parSapply, parSapplyLB
## The following objects are masked from 'package:stats':
##
## IQR, mad, xtabs
## The following objects are masked from 'package:base':
##
## Filter, Find, Map, Position, Reduce, anyDuplicated, append,
## as.data.frame, cbind, colnames, do.call, duplicated, eval,
## evalq, get, grep, grepl, intersect, is.unsorted, lapply,
## lengths, mapply, match, mget, order, paste, pmax, pmax.int,
## pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, sort,
## table, tapply, union, unique, unsplit, which, which.max,
## which.min
## Loading required package: AnnotationHub
## Loading required package: ExperimentHubData
## Loading required package: S4Vectors
## Loading required package: stats4
##
## Attaching package: 'S4Vectors'
## The following objects are masked from 'package:base':
##
## colMeans, colSums, expand.grid, rowMeans, rowSums
## Loading required package: AnnotationHubData
## Loading required package: IRanges
## Loading required package: GenomicRanges
## Loading required package: GenomeInfoDb
## Setting options('download.file.method.GEOquery'='auto')
## Setting options('GEOquery.inmemory.gpl'=FALSE)
This package contains the following four GAlignmentPairs objects. We can access these directly with named functions:
ERR188297()
## snapshotDate(): 2016-08-08
## see ?alpineData and browseVignettes('alpineData') for documentation
## loading from cache '/home/biocbuild//.ExperimentHub/166'
## GAlignmentPairs object with 25531 pairs, strandMode=1, and 0 metadata columns:
## seqnames strand : ranges --
## <Rle> <Rle> : <IRanges> --
## [1] 1 + : [108560389, 108560463] --
## [2] 1 - : [108560454, 108560528] --
## [3] 1 + : [108560534, 108600608] --
## [4] 1 - : [108569920, 108569994] --
## [5] 1 - : [108587954, 108588028] --
## ... ... ... ... ... ...
## [25527] X + : [119790596, 119790670] --
## [25528] X + : [119790988, 119791062] --
## [25529] X + : [119791037, 119791111] --
## [25530] X + : [119791348, 119791422] --
## [25531] X + : [119791376, 119791450] --
## ranges
## <IRanges>
## [1] [108560454, 108560528]
## [2] [108560383, 108560457]
## [3] [108600626, 108606236]
## [4] [108569825, 108569899]
## [5] [108587881, 108587955]
## ... ...
## [25527] [119790717, 119790791]
## [25528] [119791086, 119791160]
## [25529] [119791142, 119791216]
## [25530] [119791475, 119791549]
## [25531] [119791481, 119791555]
## -------
## seqinfo: 194 sequences from an unspecified genome
ERR188088()
## snapshotDate(): 2016-08-08
## see ?alpineData and browseVignettes('alpineData') for documentation
## loading from cache '/home/biocbuild//.ExperimentHub/167'
## GAlignmentPairs object with 28576 pairs, strandMode=1, and 0 metadata columns:
## seqnames strand : ranges --
## <Rle> <Rle> : <IRanges> --
## [1] 1 - : [108565979, 108566053] --
## [2] 1 - : [108573341, 108573415] --
## [3] 1 + : [108581087, 108581161] --
## [4] 1 + : [108601105, 108601179] --
## [5] 1 - : [108603628, 108603701] --
## ... ... ... ... ... ...
## [28572] X - : [119791266, 119791340] --
## [28573] X - : [119791431, 119791505] --
## [28574] X - : [119791593, 119791667] --
## [28575] X - : [119791629, 119791703] --
## [28576] X - : [119791637, 119791711] --
## ranges
## <IRanges>
## [1] [108565846, 108565920]
## [2] [108573234, 108573308]
## [3] [108581239, 108581313]
## [4] [108601196, 108601270]
## [5] [108603540, 108603614]
## ... ...
## [28572] [119791130, 119791204]
## [28573] [119791358, 119791432]
## [28574] [119786691, 119789940]
## [28575] [119789951, 119791587]
## [28576] [119789976, 119791612]
## -------
## seqinfo: 194 sequences from an unspecified genome
ERR188204()
## snapshotDate(): 2016-08-08
## see ?alpineData and browseVignettes('alpineData') for documentation
## loading from cache '/home/biocbuild//.ExperimentHub/168'
## GAlignmentPairs object with 35079 pairs, strandMode=1, and 0 metadata columns:
## seqnames strand : ranges --
## <Rle> <Rle> : <IRanges> --
## [1] 1 + : [108560441, 108560516] --
## [2] 1 + : [108560442, 108560517] --
## [3] 1 + : [108560443, 108560518] --
## [4] 1 + : [108560447, 108560522] --
## [5] 1 + : [108560500, 108600570] --
## ... ... ... ... ... ...
## [35075] X - : [119790855, 119790930] --
## [35076] X - : [119791108, 119791183] --
## [35077] X - : [119791575, 119791650] --
## [35078] X - : [119791593, 119791668] --
## [35079] X - : [119791627, 119791702] --
## ranges
## <IRanges>
## [1] [108600607, 108600682]
## [2] [108560519, 108600594]
## [3] [108560485, 108560560]
## [4] [108560517, 108600592]
## [5] [108600586, 108600660]
## ... ...
## [35075] [119790578, 119790653]
## [35076] [119791047, 119791122]
## [35077] [119786574, 119786649]
## [35078] [119789978, 119791613]
## [35079] [119791585, 119791660]
## -------
## seqinfo: 194 sequences from an unspecified genome
ERR188317()
## snapshotDate(): 2016-08-08
## see ?alpineData and browseVignettes('alpineData') for documentation
## loading from cache '/home/biocbuild//.ExperimentHub/169'
## GAlignmentPairs object with 44535 pairs, strandMode=1, and 0 metadata columns:
## seqnames strand : ranges --
## <Rle> <Rle> : <IRanges> --
## [1] 1 + : [108560515, 108600590] --
## [2] 1 - : [108560530, 108600605] --
## [3] 1 + : [108560533, 108600608] --
## [4] 1 + : [108560552, 108600627] --
## [5] 1 + : [108575456, 108575531] --
## ... ... ... ... ... ...
## [44531] X - : [119791460, 119791535] --
## [44532] X - : [119791574, 119791649] --
## [44533] X - : [119791574, 119791649] --
## [44534] X - : [119791585, 119791660] --
## [44535] X - : [119791620, 119791695] --
## ranges
## <IRanges>
## [1] [108600611, 108600686]
## [2] [108560452, 108560527]
## [3] [108612199, 108612274]
## [4] [108606221, 108612221]
## [5] [108575548, 108575623]
## ... ...
## [44531] [119791348, 119791423]
## [44532] [119786691, 119789941]
## [44533] [119789953, 119791590]
## [44534] [119789990, 119791613]
## [44535] [119789953, 119791590]
## -------
## seqinfo: 194 sequences from an unspecified genome
Or we can access them using the ExperimentHub interface:
eh <- ExperimentHub()
## snapshotDate(): 2016-08-08
query(eh, "ERR188")
## ExperimentHub with 4 records
## # snapshotDate(): 2016-08-08
## # $dataprovider: GEUVADIS
## # $species: Homo sapiens
## # $rdataclass: GAlignmentPairs
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass,
## # tags, sourceurl, sourcetype
## # retrieve records with, e.g., 'object[["EH166"]]'
##
## title
## EH166 | ERR188297
## EH167 | ERR188088
## EH168 | ERR188204
## EH169 | ERR188317
eh[["EH166"]]
## see ?alpineData and browseVignettes('alpineData') for documentation
## loading from cache '/home/biocbuild//.ExperimentHub/166'
## GAlignmentPairs object with 25531 pairs, strandMode=1, and 0 metadata columns:
## seqnames strand : ranges --
## <Rle> <Rle> : <IRanges> --
## [1] 1 + : [108560389, 108560463] --
## [2] 1 - : [108560454, 108560528] --
## [3] 1 + : [108560534, 108600608] --
## [4] 1 - : [108569920, 108569994] --
## [5] 1 - : [108587954, 108588028] --
## ... ... ... ... ... ...
## [25527] X + : [119790596, 119790670] --
## [25528] X + : [119790988, 119791062] --
## [25529] X + : [119791037, 119791111] --
## [25530] X + : [119791348, 119791422] --
## [25531] X + : [119791376, 119791450] --
## ranges
## <IRanges>
## [1] [108560454, 108560528]
## [2] [108560383, 108560457]
## [3] [108600626, 108606236]
## [4] [108569825, 108569899]
## [5] [108587881, 108587955]
## ... ...
## [25527] [119790717, 119790791]
## [25528] [119791086, 119791160]
## [25529] [119791142, 119791216]
## [25530] [119791475, 119791549]
## [25531] [119791481, 119791555]
## -------
## seqinfo: 194 sequences from an unspecified genome
For details on the source of these files, and on their construction
see ?alpineData and the scripts:
inst/scripts/make-metadata.Rinst/scripts/make-data.RmdWe can take a quick look at the paired alignments from one file. For example their distribution on the different chromosomes:
library(GenomicAlignments)
## Loading required package: SummarizedExperiment
## Loading required package: Biobase
## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.
##
## Attaching package: 'Biobase'
## The following object is masked from 'package:ExperimentHub':
##
## cache
## The following object is masked from 'package:AnnotationHub':
##
## cache
## Loading required package: Biostrings
## Loading required package: XVector
## Loading required package: Rsamtools
gap <- ERR188297()
## snapshotDate(): 2016-08-08
## see ?alpineData and browseVignettes('alpineData') for documentation
## loading from cache '/home/biocbuild//.ExperimentHub/166'
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")
