---
title: "1. Introduction to _R_"
author: "Valerie Obenchain (valerie.obenchain@roswellpark.org)<br />
    Lori Shepherd (lori.shepherd@roswellpark.org)<br />
    Martin Morgan (martin.morgan@roswellpark.org)<br />
    Stanford University, Stanford, CA<br />
    25 - 26 June, 2016"
output:
  BiocStyle::html_document:
    toc: true
    toc_depth: 2
vignette: >
  % \VignetteIndexEntry{1. Introduction to _R_}
  % \VignetteEngine{knitr::rmarkdown}
---

```{r style, echo = FALSE, results = 'asis'}
BiocStyle::markdown()
options(width=100, max.print=1000)
knitr::opts_chunk$set(
    eval=as.logical(Sys.getenv("KNITR_EVAL", "TRUE")),
    cache=as.logical(Sys.getenv("KNITR_CACHE", "TRUE")))
```

```{r packages, eval=TRUE, echo=FALSE, warning=FALSE, message=FALSE}
suppressPackageStartupMessages({
    library(BioC2016Introduction)
    library(SummarizedExperiment)
    library(airway)
})
```

The material in this course requires R version 3.3 and Bioconductor
version 3.4

```{r configure-test}
stopifnot(
    getRversion() >= '3.3' && getRversion() < '3.4',
    BiocInstaller::biocVersion() == "3.4"
)
```

Version: `r packageDescription("BioC2016Introduction")$Version`<br />
Compiled: `r date()`

# _R_

Language and environment for statistical computing and graphics

- Full-featured programming language
- Interactive and *interpretted* -- convenient and forgiving
- Coherent, extensive documentation
- Statistical, e.g. `factor()`, `NA`
- Extensible -- CRAN, Bioconductor, github, ...

## Vectors, classes, objects

- Efficient _vectorized_ calculations on 'atomic' vectors `logical`,
  `integer`, `numeric`, `complex`, `character`, `byte`
- Atomic vectors are building blocks for more complicated _objects_
  - `matrix` -- atomic vector with 'dim' attribute
  - `data.frame` -- list of equal length atomic vectors
- Formal _classes_ represent complicated combinations of vectors,
  e.g., the return value of `lm()`, below

## Functions, generics, methods

- Functions transform inputs to outputs, perhaps with side effects,
  e.g., `rnorm(1000)`
  - Argument matching first by name, then by position
  - Functions may define (some) arguments to have default values
- _Generic_ functions dispatch to specific _methods_ based on class of
  argument(s), e.g., `print()`. 
- Methods are functions that implement specific generics, e.g.,
  `print.factor`; methods are invoked _indirectly_, via the generic.

## Introspection

- General properties, e.g., `class()`, `str()`
- Class-specific properties, e.g., `dim()`

## Help

- `?print`: help on the generic print 
- `?print.data.frame`: help on print method for objects of class
    data.frame.

Example

```{r}
x <- rnorm(1000)                   # atomic vectors
y <- x + rnorm(1000, sd=.5)
df <- data.frame(x=x, y=y)         # object of class 'data.frame'
plot(y ~ x, df)                    # generic plot, method plot.formula
fit <- lm(y ~x, df)                # object of class 'lm'
methods(class=class(fit))          # introspection
```

# Resources

- [Web site](https://www.r-project.org/) -- install, learn, use, develop
- [Manuals](https://cran.r-project.org/manuals.html)
- [Mailing list support](https://www.r-project.org/mail.html) -- seek help and
  guidance; also
  [StackOverflow](http://stackoverflow.com/questions/tagged/r) for _R_
  programming questions
- [Hadley Wickham's Advanced R book](http://adv-r.had.co.nz/)

Acknowledgements

  The research reported in this presentation was supported by the
  National Cancer Institute and the National Human Genome Research
  Institute of the National Institutes of Health under Award numbers
  U24CA180996 and U41HG004059, and the National Science Foundation
  under Award number 1247813. The content is solely the responsibility
  of the authors and does not necessarily represent the official views
  of the National Institutes of Health or the National Science
  Foundation.

## `sessionInfo()`

```{r sessionInfo}
sessionInfo()
```

<!-- Bibliography -->

[R]: http://r-project.org
[Bioconductor]: http://bioconductor.org
[GRanges.bib]: http://dx.doi.org/10.1371/journal.pcbi.1003118
[Scalable.bib]: http://arxiv.org/abs/1409.2864
[Lawrence.bioc2014.bib]:
    http://bioconductor.org/help/course-materials/2014/BioC2014/Lawrence_Talk.pdf


[AnnotationData]: http://bioconductor.org/packages/release/BiocViews.html#___AnnotationData
[biocViews]: http://bioconductor.org/packages/release/BiocViews.html#___Software

[AnnotationDbi]: http://bioconductor.org/packages/AnnotationDbi
[AnnotationHub]: http://bioconductor.org/packages/AnnotationHub
[BSgenome.Hsapiens.UCSC.hg19]: http://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19
[BSgenome]: http://bioconductor.org/packages/BSgenome
[BiocParallel]: http://bioconductor.org/packages/BiocParallel
[Biostrings]: http://bioconductor.org/packages/Biostrings
[CNTools]: http://bioconductor.org/packages/CNTools
[ChIPQC]: http://bioconductor.org/packages/ChIPQC
[ChIPseeker]: http://bioconductor.org/packages/ChIPseeker
[DESeq2]: http://bioconductor.org/packages/DESeq2
[DiffBind]: http://bioconductor.org/packages/DiffBind
[GenomicAlignments]: http://bioconductor.org/packages/GenomicAlignments
[GenomicFiles]: http://bioconductor.org/packages/GenomicFiles
[GenomicRanges]: http://bioconductor.org/packages/GenomicRanges
[Homo.sapiens]: http://bioconductor.org/packages/Homo.sapiens
[IRanges]: http://bioconductor.org/packages/IRanges
[KEGGREST]: http://bioconductor.org/packages/KEGGREST
[PSICQUIC]: http://bioconductor.org/packages/PSICQUIC
[Rsamtools]: http://bioconductor.org/packages/Rsamtools
[Rsubread]: http://bioconductor.org/packages/Rsubread
[ShortRead]: http://bioconductor.org/packages/ShortRead
[SomaticSignatures]: http://bioconductor.org/packages/SomaticSignatures
[SummarizedExperiment]: http://bioconductor.org/packages/SummarizedExperiment
[TxDb.Hsapiens.UCSC.hg19.knownGene]: http://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene
[VariantAnnotation]: http://bioconductor.org/packages/VariantAnnotation
[VariantFiltering]: http://bioconductor.org/packages/VariantFiltering
[VariantTools]: http://bioconductor.org/packages/VariantTools
[biomaRt]: http://bioconductor.org/packages/biomaRt
[cn.mops]: http://bioconductor.org/packages/cn.mops
[csaw]: http://bioconductor.org/packages/csaw
[edgeR]: http://bioconductor.org/packages/edgeR
[ensemblVEP]: http://bioconductor.org/packages/ensemblVEP 
[h5vc]: http://bioconductor.org/packages/h5vc
[limma]: http://bioconductor.org/packages/limma
[metagenomeSeq]: http://bioconductor.org/packages/metagenomeSeq
[org.Hs.eg.db]: http://bioconductor.org/packages/org.Hs.eg.db
[org.Sc.sgd.db]: http://bioconductor.org/packages/org.Sc.sgd.db
[phyloseq]: http://bioconductor.org/packages/phyloseq
[rtracklayer]: http://bioconductor.org/packages/rtracklayer
[snpStats]: http://bioconductor.org/packages/snpStats
[Gviz]: http://bioconductor.org/packages/Gviz
[epivizr]: http://bioconductor.org/packages/epivizr
[ggbio]: http://bioconductor.org/packages/ggbio
[OmicCircos]: http://bioconductor.org/packages/OmicCircos

[dplyr]: https://cran.r-project.org/package=dplyr
[data.table]: https://cran.r-project.org/package=data.table
[Rcpp]: https://cran.r-project.org/package=Rcpp

[AMI]: http://bioconductor.org/help/bioconductor-cloud-ami/
[docker]: http://bioconductor.org/help/docker/