Exploring the GAlignmentPairs in alpineData

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, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
##     as.data.frame, cbind, colMeans, colSums, 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, rowMeans,
##     rowSums, rownames, sapply, setdiff, sort, table, tapply,
##     union, unique, unsplit, which, which.max, which.min
## Loading required package: AnnotationHub

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

ERR188297()
## snapshotDate(): 2016-12-12
## see ?alpineData and browseVignettes('alpineData') for documentation
## loading from cache '/home/biocbuild//.ExperimentHub/166'
## Loading required package: GenomicAlignments
## Loading required package: S4Vectors
## Loading required package: stats4
## 
## Attaching package: 'S4Vectors'
## The following object is masked from 'package:base':
## 
##     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':
## 
##     cache
## The following object is masked from 'package:AnnotationHub':
## 
##     cache
## Loading required package: DelayedArray
## Loading required package: matrixStats
## 
## Attaching package: 'matrixStats'
## The following objects are masked from 'package:Biobase':
## 
##     anyMissing, rowMedians
## 
## Attaching package: 'DelayedArray'
## The following objects are masked from 'package:matrixStats':
## 
##     colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
## The following object is masked from 'package:base':
## 
##     apply
## Loading required package: Biostrings
## Loading required package: XVector
## 
## Attaching package: 'Biostrings'
## The following object is masked from 'package:DelayedArray':
## 
##     type
## The following object is masked from 'package:base':
## 
##     strsplit
## Loading required package: Rsamtools
## 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(): 2016-12-12
## 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(): 2016-12-12
## 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(): 2016-12-12
## 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(): 2016-12-12
query(eh, "ERR188")
## ExperimentHub with 4 records
## # snapshotDate(): 2016-12-12 
## # $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
## 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:

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()
## snapshotDate(): 2016-12-12
## 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")

plot of chunk unnamed-chunk-4

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")
## Warning in n * h: NAs produced by integer overflow

plot of chunk unnamed-chunk-5