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vjcitn committed Sep 16, 2013
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Expand Up @@ -66,251 +66,57 @@ a yeast microarray probe.

First, we obtain the reference genomic sequence
for sacCer2 version of yeast.

```r
```{r lkg}
library(BSgenome.Scerevisiae.UCSC.sacCer2)
```

```
## Loading required package: BSgenome 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 object is masked from 'package:stats':
##
## xtabs
##
## The following objects are masked from 'package:base':
##
## anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
## duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply,
## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
## rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply,
## union, unique, unlist
##
## Loading required package: IRanges Loading required package: GenomicRanges
## Loading required package: XVector Loading required package: Biostrings
```

```r
class(Scerevisiae)
```

```
## [1] "BSgenome"
## attr(,"package")
## [1] "BSgenome"
```

```r
Scerevisiae
```

```
## Yeast genome
## |
## | organism: Saccharomyces cerevisiae (Yeast)
## | provider: UCSC
## | provider version: sacCer2
## | release date: June 2008
## | release name: SGD June 2008 sequence
## |
## | sequences (see '?seqnames'):
## | chrI chrII chrIII chrIV chrV chrVI chrVII chrVIII
## | chrIX chrX chrXI chrXII chrXIII chrXIV chrXV chrXVI
## | chrM 2micron
## |
## | (use the '$' or '[[' operator to access a given sequence)
```


We focus attention on chrIV for now.

```r
```{r doc4}
c4 = Scerevisiae$chrIV
class(c4)
```

```
## [1] "DNAString"
## attr(,"package")
## [1] "Biostrings"
```

```r
c4
```

```
## 1531919-letter "DNAString" instance
## seq: ACACCACACCCACACCACACCCACACACACCACA...AAACATAAAATAAAGGTAGTAAGTAGCTTTTGG
```


Now we obtain the probe and annotation data for
the Affy yeast2 array.

```r
```{r getp}
library(yeast2.db)
```

```
## Loading required package: AnnotationDbi 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: 'AnnotationDbi'
##
## The following object is masked from 'package:BSgenome':
##
## species
##
## Loading required package: org.Sc.sgd.db Loading required package: DBI
```

```r
library(yeast2probe)
yeast2probe[1:3, ]
yeast2probe[1:3,]
```

```
## sequence x y Probe.Set.Name
## 1 GAAAGTTTCAGTGCACGTCTTCAAA 380 257 1769438_at
## 2 GTATATTTCTAATCTTCCTCTTCAT 28 327 1769438_at
## 3 ATATCAAACCGCGTACTTCGTGACT 188 19 1769438_at
## Probe.Interrogation.Position Target.Strandedness
## 1 1117 Antisense
## 2 1170 Antisense
## 3 1240 Antisense
```


We'll pick one probe set, and then the sequence of one probe.

```r
ypick = yeast2probe[yeast2probe$Probe.Set.Name == "1769311_at", ]
```{r getps}
ypick = yeast2probe[yeast2probe$Probe.Set.Name=="1769311_at",]
dim(ypick)
```

```
## [1] 11 6
```

```r
ypick[1:3, ]
```

```
## sequence x y Probe.Set.Name
## 1959 ATGAGCACTATGTTTTCTGTTGGAT 486 39 1769311_at
## 1960 GTTTTCTGTTGGATTTGGCTCATAC 154 321 1769311_at
## 1961 TTGGCTCATACTTGGCATCTGGGAA 20 493 1769311_at
## Probe.Interrogation.Position Target.Strandedness
## 1959 100 Antisense
## 1960 111 Antisense
## 1961 125 Antisense
```

```r
ypick[1:3,]
a = "ATGAGCACTATGTTTTCTGTTGGAT"
ra = reverseComplement(DNAString(a))
```


Now we use the simple lookup of Biostrings.

```r
```{r getm}
matchPattern(ra, c4)
```

```
## Views on a 1531919-letter DNAString subject
## subject: ACACCACACCCACACCACACCCACACACACCA...ACATAAAATAAAGGTAGTAAGTAGCTTTTGG
## views:
## start end width
## [1] 174478 174502 25 [ATCCAACAGAAAACATAGTGCTCAT]
```

```r
get("1769311_at", yeast2CHRLOC)
```

```
## 4
## -174232
```

```r
get("1769311_at", yeast2CHRLOCEND)
```

```
## 4
## -174588
```


Exercise. Discuss how to identify probes harboring SNP in the
affy u133plus2 array.


<h3>ExpressionSet and self-description</h3>

The <code>ExpressionSet</code> class unifies information on a microarray experiment.

```r
```{r lkall}
library(ALL)
data(ALL)
getClass(class(ALL))
```

```
## Class "ExpressionSet" [package "Biobase"]
##
## Slots:
##
## Name: experimentData assayData phenoData
## Class: MIAME AssayData AnnotatedDataFrame
##
## Name: featureData annotation protocolData
## Class: AnnotatedDataFrame character AnnotatedDataFrame
##
## Name: .__classVersion__
## Class: Versions
##
## Extends:
## Class "eSet", directly
## Class "VersionedBiobase", by class "eSet", distance 2
## Class "Versioned", by class "eSet", distance 3
```

```r
experimentData(ALL)
```

```
## Experiment data
## Experimenter name: Chiaretti et al.
## Laboratory: Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
## Contact information:
## Title: Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival.
## URL:
## PMIDs: 14684422 16243790
##
## Abstract: A 187 word abstract is available. Use 'abstract' method.
```


A very high-level aspect of self-description is the facility for
binding information on the publication of expression data to
the data object itself. The <code>abstract</code> method gives
Expand Down Expand Up @@ -343,15 +149,13 @@ to the genomic location of the read or probe for interpretation. The

A large-scale illustration of this class is in the \textit{dsQTL}
package, but it is very large so I do not require that you download it.

```r
```{r lkdsq,eval=FALSE}
library(dsQTL)
data(DSQ_17)
DSQ_17
rowData(DSQ_17)[1:3]
```


You can use \verb+example("SummarizedExperiment-class")+ to
get a working minimal example.

Expand All @@ -361,57 +165,13 @@ subscripting still selects samples.

The <code>VCF</code> class extends <code>SummarizedExperiment</code>
to manage information on variant calls on a number of samples.

```r
```{r lkv}
library(VariantAnnotation)
```

```
## Loading required package: Rsamtools
##
## Attaching package: 'VariantAnnotation'
##
## The following object is masked from 'package:base':
##
## tabulate
```

```r
fl <- system.file("extdata", "structural.vcf", package = "VariantAnnotation")
vcf <- readVcf(fl, genome = "hg19")
fl <- system.file("extdata", "structural.vcf", package="VariantAnnotation")
vcf <- readVcf(fl, genome="hg19")
vcf
```

```
## class: CollapsedVCF
## dim: 7 1
## rowData(vcf):
## GRanges with 5 metadata columns: paramRangeID, REF, ALT, QUAL, FILTER
## info(vcf):
## DataFrame with 10 columns: BKPTID, CIEND, CIPOS, END, HOMLEN, HOMSEQ,...
## info(header(vcf)):
## Number Type Description
## BKPTID . String ID of the assembled alternate allele in th...
## CIEND 2 Integer Confidence interval around END for impreci...
## CIPOS 2 Integer Confidence interval around POS for impreci...
## END 1 Integer End position of the variant described in t...
## HOMLEN . Integer Length of base pair identical micro-homolo...
## HOMSEQ . String Sequence of base pair identical micro-homo...
## IMPRECISE 0 Flag Imprecise structural variation
## MEINFO 4 String Mobile element info of the form NAME,START...
## SVLEN . Integer Difference in length between REF and ALT a...
## SVTYPE 1 String Type of structural variant
## geno(vcf):
## SimpleList of length 4: GT, GQ, CN, CNQ
## geno(header(vcf)):
## Number Type Description
## GT 1 String Genotype
## GQ 1 Float Genotype quality
## CN 1 Integer Copy number genotype for imprecise events
## CNQ 1 Float Copy number genotype quality for imprecise...
```


<h3>Management of information on HTS experiments</h3>


Expand Down

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