The material in this course requires R version 3.3 and Bioconductor version 3.4
stopifnot(
getRversion() >= '3.3' && getRversion() < '3.4',
BiocInstaller::biocVersion() == "3.4"
)
Version: 0.0.3
Compiled: Wed Jun 22 21:21:00 2016
Language and environment for statistical computing and graphics
factor()
, NA
logical
, integer
, numeric
, complex
, character
, byte
matrix
– atomic vector with ‘dim’ attributedata.frame
– list of equal length atomic vectorslm()
, belowrnorm(1000)
print()
.print.factor
; methods are invoked indirectly, via the generic.class()
, str()
dim()
?print
: help on the generic print?print.data.frame
: help on print method for objects of class data.frame.Example
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
## [1] add1 alias anova case.names coerce confint
## [7] cooks.distance deviance dfbeta dfbetas drop1 dummy.coef
## [13] effects extractAIC family formula fortify hatvalues
## [19] influence initialize kappa labels logLik model.frame
## [25] model.matrix nobs plot predict print proj
## [31] qr residuals rstandard rstudent show simulate
## [37] slotsFromS3 summary variable.names vcov
## see '?methods' for accessing help and source code
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()
sessionInfo()
## R version 3.3.0 (2016-05-03)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 14.04.4 LTS
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
## [4] LC_COLLATE=C LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] grid stats4 parallel stats graphics grDevices utils datasets methods
## [10] base
##
## other attached packages:
## [1] airway_0.107.2 BioC2016Introduction_0.0.3
## [3] Homo.sapiens_1.3.1 GO.db_3.3.0
## [5] OrganismDbi_1.15.1 AnnotationHub_2.5.4
## [7] Gviz_1.17.4 biomaRt_2.29.2
## [9] org.Hs.eg.db_3.3.0 BiocParallel_1.7.4
## [11] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.25.14
## [13] AnnotationDbi_1.35.3 VariantAnnotation_1.19.2
## [15] RNAseqData.HNRNPC.bam.chr14_0.11.0 GenomicAlignments_1.9.4
## [17] Rsamtools_1.25.0 SummarizedExperiment_1.3.5
## [19] Biobase_2.33.0 BSgenome.Hsapiens.UCSC.hg19_1.4.0
## [21] BSgenome_1.41.2 rtracklayer_1.33.7
## [23] GenomicRanges_1.25.8 GenomeInfoDb_1.9.1
## [25] Biostrings_2.41.4 XVector_0.13.2
## [27] IRanges_2.7.11 S4Vectors_0.11.7
## [29] BiocGenerics_0.19.1 ggplot2_2.1.0
## [31] BiocStyle_2.1.10
##
## loaded via a namespace (and not attached):
## [1] httr_1.2.0 splines_3.3.0 Formula_1.2-1
## [4] shiny_0.13.2 interactiveDisplayBase_1.11.3 latticeExtra_0.6-28
## [7] RBGL_1.49.1 yaml_2.1.13 RSQLite_1.0.0
## [10] lattice_0.20-33 biovizBase_1.21.0 chron_2.3-47
## [13] digest_0.6.9 RColorBrewer_1.1-2 colorspace_1.2-6
## [16] htmltools_0.3.5 httpuv_1.3.3 Matrix_1.2-6
## [19] plyr_1.8.4 XML_3.98-1.4 zlibbioc_1.19.0
## [22] xtable_1.8-2 scales_0.4.0 nnet_7.3-12
## [25] survival_2.39-4 magrittr_1.5 mime_0.4
## [28] evaluate_0.9 foreign_0.8-66 graph_1.51.0
## [31] BiocInstaller_1.23.4 tools_3.3.0 data.table_1.9.6
## [34] formatR_1.4 matrixStats_0.50.2 stringr_1.0.0
## [37] munsell_0.4.3 cluster_2.0.4 ensembldb_1.5.8
## [40] RCurl_1.95-4.8 dichromat_2.0-0 bitops_1.0-6
## [43] labeling_0.3 rmarkdown_0.9.6 gtable_0.2.0
## [46] codetools_0.2-14 DBI_0.4-1 reshape2_1.4.1
## [49] R6_2.1.2 gridExtra_2.2.1 knitr_1.13
## [52] Hmisc_3.17-4 stringi_1.1.1 Rcpp_0.12.5
## [55] rpart_4.1-10 acepack_1.3-3.3