Dear List,

	I am working through the use case in the easyRNASeq 
vignette with the human data (section 6 of the vignette).
I am not sure where the bam files are for the use case. 

Here is the record of my session:

> library(easyRNASeq)
Loading required package: parallel
Loading required package: genomeIntervals
Loading required package: intervals
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

    xtabs

The following object(s) are masked from ‘package:base’:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map,
    mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

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")'.

Loading required package: biomaRt
Loading required package: edgeR
Loading required package: limma
Loading required package: Biostrings
Loading required package: IRanges

Attaching package: ‘IRanges’

The following object(s) are masked from ‘package:intervals’:

    reduce


Attaching package: ‘Biostrings’

The following object(s) are masked from ‘package:intervals’:

    type

Loading required package: BSgenome
Loading required package: GenomicRanges
Loading required package: DESeq
Loading required package: locfit
locfit 1.5-8 	 2012-04-25

Attaching package: ‘locfit’

The following object(s) are masked from ‘package:GenomicRanges’:

    left, right

Loading required package: Rsamtools
Loading required package: ShortRead
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer
Warning messages:
1: replacing previous import ‘coerce’ when loading ‘intervals’ 
2: replacing previous import ‘initialize’ when loading ‘intervals’ 
> library(BSgenome.Hsapiens.UCSC.hg19)
> chr.sizes=as.list(seqlengths(Hsapiens))
> class(chr.sizes)
[1] "list"
> bamfiles=dir(getwd(),pattern="*\\.bam$")
> bamfiles
character(0)
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.3.17 easyRNASeq_1.2.3                   ShortRead_1.14.4                  
 [4] latticeExtra_0.6-19                RColorBrewer_1.0-5                 lattice_0.20-6                    
 [7] Rsamtools_1.8.5                    DESeq_1.8.3                        locfit_1.5-8                      
[10] BSgenome_1.24.0                    GenomicRanges_1.8.7                Biostrings_2.24.1                 
[13] IRanges_1.14.4                     edgeR_2.6.10                       limma_3.12.1                      
[16] biomaRt_2.12.0                     Biobase_2.16.0                     genomeIntervals_1.12.0            
[19] BiocGenerics_0.2.0                 intervals_0.13.3                  

loaded via a namespace (and not attached):
 [1] annotate_1.34.1      AnnotationDbi_1.18.1 bitops_1.0-4.1       DBI_0.2-5            genefilter_1.38.0   
 [6] geneplotter_1.34.0   grid_2.15.1          hwriter_1.3          RCurl_1.91-1         RSQLite_0.11.1      
[11] splines_2.15.1       stats4_2.15.1        survival_2.36-14     XML_3.9-4            xtable_1.7-0        
[16] zlibbioc_1.2.0      
> 

THANKS!
Rich


Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman@cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

"School is an evil plot to suppress my individuality"

Rose Friedman, age15


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