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':
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## IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
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## Filter, Find, Map, Position, Reduce, anyDuplicated, append,
## as.data.frame, basename, cbind, colnames, dirname, do.call,
## duplicated, eval, evalq, get, grep, grepl, intersect,
## is.unsorted, lapply, 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: BiocFileCache
## Loading required package: dbplyr
## Loading required package: GenomicAlignments
## Loading required package: S4Vectors
## Loading required package: stats4
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## Attaching package: 'S4Vectors'
## The following object is masked from 'package:base':
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## expand.grid
## Loading required package: IRanges
## Loading required package: GenomeInfoDb
## Loading required package: GenomicRanges
## 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':
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## cache
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## cache
## Loading required package: DelayedArray
## Loading required package: matrixStats
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## Attaching package: 'matrixStats'
## The following objects are masked from 'package:Biobase':
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## anyMissing, rowMedians
## Loading required package: BiocParallel
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## Attaching package: 'DelayedArray'
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## aperm, apply, rowsum
## Loading required package: Biostrings
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## Attaching package: 'Biostrings'
## The following object is masked from 'package:DelayedArray':
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## type
## The following object is masked from 'package:base':
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## strsplit
## Loading required package: Rsamtools
This package contains the following four GAlignmentPairs objects. We can access these directly with named functions:
ERR188297()
## snapshotDate(): 2019-04-29
## see ?alpineData and browseVignettes('alpineData') for documentation
## downloading 0 resources
## loading from cache
## 'EH166 : 166'
## GAlignmentPairs object with 25531 pairs, strandMode=1, and 0 metadata columns:
## seqnames strand : ranges -- ranges
## <Rle> <Rle> : <IRanges> -- <IRanges>
## [1] 1 + : 108560389-108560463 -- 108560454-108560528
## [2] 1 - : 108560454-108560528 -- 108560383-108560457
## [3] 1 + : 108560534-108600608 -- 108600626-108606236
## [4] 1 - : 108569920-108569994 -- 108569825-108569899
## [5] 1 - : 108587954-108588028 -- 108587881-108587955
## ... ... ... ... ... ... ...
## [25527] X + : 119790596-119790670 -- 119790717-119790791
## [25528] X + : 119790988-119791062 -- 119791086-119791160
## [25529] X + : 119791037-119791111 -- 119791142-119791216
## [25530] X + : 119791348-119791422 -- 119791475-119791549
## [25531] X + : 119791376-119791450 -- 119791481-119791555
## -------
## seqinfo: 194 sequences from an unspecified genome
ERR188088()
## snapshotDate(): 2019-04-29
## see ?alpineData and browseVignettes('alpineData') for documentation
## downloading 0 resources
## loading from cache
## 'EH167 : 167'
## GAlignmentPairs object with 28576 pairs, strandMode=1, and 0 metadata columns:
## seqnames strand : ranges -- ranges
## <Rle> <Rle> : <IRanges> -- <IRanges>
## [1] 1 - : 108565979-108566053 -- 108565846-108565920
## [2] 1 - : 108573341-108573415 -- 108573234-108573308
## [3] 1 + : 108581087-108581161 -- 108581239-108581313
## [4] 1 + : 108601105-108601179 -- 108601196-108601270
## [5] 1 - : 108603628-108603701 -- 108603540-108603614
## ... ... ... ... ... ... ...
## [28572] X - : 119791266-119791340 -- 119791130-119791204
## [28573] X - : 119791431-119791505 -- 119791358-119791432
## [28574] X - : 119791593-119791667 -- 119786691-119789940
## [28575] X - : 119791629-119791703 -- 119789951-119791587
## [28576] X - : 119791637-119791711 -- 119789976-119791612
## -------
## seqinfo: 194 sequences from an unspecified genome
ERR188204()
## snapshotDate(): 2019-04-29
## see ?alpineData and browseVignettes('alpineData') for documentation
## downloading 0 resources
## loading from cache
## 'EH168 : 168'
## GAlignmentPairs object with 35079 pairs, strandMode=1, and 0 metadata columns:
## seqnames strand : ranges -- ranges
## <Rle> <Rle> : <IRanges> -- <IRanges>
## [1] 1 + : 108560441-108560516 -- 108600607-108600682
## [2] 1 + : 108560442-108560517 -- 108560519-108600594
## [3] 1 + : 108560443-108560518 -- 108560485-108560560
## [4] 1 + : 108560447-108560522 -- 108560517-108600592
## [5] 1 + : 108560500-108600570 -- 108600586-108600660
## ... ... ... ... ... ... ...
## [35075] X - : 119790855-119790930 -- 119790578-119790653
## [35076] X - : 119791108-119791183 -- 119791047-119791122
## [35077] X - : 119791575-119791650 -- 119786574-119786649
## [35078] X - : 119791593-119791668 -- 119789978-119791613
## [35079] X - : 119791627-119791702 -- 119791585-119791660
## -------
## seqinfo: 194 sequences from an unspecified genome
ERR188317()
## snapshotDate(): 2019-04-29
## see ?alpineData and browseVignettes('alpineData') for documentation
## downloading 0 resources
## loading from cache
## 'EH169 : 169'
## GAlignmentPairs object with 44535 pairs, strandMode=1, and 0 metadata columns:
## seqnames strand : ranges -- ranges
## <Rle> <Rle> : <IRanges> -- <IRanges>
## [1] 1 + : 108560515-108600590 -- 108600611-108600686
## [2] 1 - : 108560530-108600605 -- 108560452-108560527
## [3] 1 + : 108560533-108600608 -- 108612199-108612274
## [4] 1 + : 108560552-108600627 -- 108606221-108612221
## [5] 1 + : 108575456-108575531 -- 108575548-108575623
## ... ... ... ... ... ... ...
## [44531] X - : 119791460-119791535 -- 119791348-119791423
## [44532] X - : 119791574-119791649 -- 119786691-119789941
## [44533] X - : 119791574-119791649 -- 119789953-119791590
## [44534] X - : 119791585-119791660 -- 119789990-119791613
## [44535] X - : 119791620-119791695 -- 119789953-119791590
## -------
## seqinfo: 194 sequences from an unspecified genome
Or we can access them using the ExperimentHub interface:
eh <- ExperimentHub()
## snapshotDate(): 2019-04-29
query(eh, "ERR188")
## ExperimentHub with 4 records
## # snapshotDate(): 2019-04-29
## # $dataprovider: GEUVADIS
## # $species: Homo sapiens
## # $rdataclass: GAlignmentPairs
## # additional mcols(): taxonomyid, genome, description,
## # coordinate_1_based, maintainer, rdatadateadded, preparerclass,
## # tags, rdatapath, 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
## downloading 0 resources
## loading from cache
## 'EH166 : 166'
## GAlignmentPairs object with 25531 pairs, strandMode=1, and 0 metadata columns:
## seqnames strand : ranges -- ranges
## <Rle> <Rle> : <IRanges> -- <IRanges>
## [1] 1 + : 108560389-108560463 -- 108560454-108560528
## [2] 1 - : 108560454-108560528 -- 108560383-108560457
## [3] 1 + : 108560534-108600608 -- 108600626-108606236
## [4] 1 - : 108569920-108569994 -- 108569825-108569899
## [5] 1 - : 108587954-108588028 -- 108587881-108587955
## ... ... ... ... ... ... ...
## [25527] X + : 119790596-119790670 -- 119790717-119790791
## [25528] X + : 119790988-119791062 -- 119791086-119791160
## [25529] X + : 119791037-119791111 -- 119791142-119791216
## [25530] X + : 119791348-119791422 -- 119791475-119791549
## [25531] X + : 119791376-119791450 -- 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)
gap <- ERR188297()
## snapshotDate(): 2019-04-29
## see ?alpineData and browseVignettes('alpineData') for documentation
## downloading 0 resources
## loading from cache
## 'EH166 : 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")
