[BioC] assignChromosomeRegion in 2.6.0 ChIPpeakAnno

[Zhu, Lihua (Julie)]

Stefan,

Could you please send me the sessionInfo? I just want to make sure you
installed version 2.6.0. Thanks!

I noticed that when I try to install ChIPpeakAnno with the following code, I
get 2.4 version instead.

source("http://bioconductor.org/biocLite.R")
biocLite("ChIPpeakAnno")

Best regards,

Julie


On 3/14/13 8:02 PM, "Stefan Pinter" <pinter at molbio.mgh.harvard.edu> wrote:

> Dear Julie,
> 
> I apologize for emailing you about this directly, but I'm in a bit of
> time-crunch, otherwise I'd post this to the mailing list. I'm using
> ChIPpeakAnno (see installed packages below), and while the other functions
> I've tested (BED2Ranges, annotatePeakInBatch, getAnnotation) in your package
> (2.6.0) work, assignChromosomeRegion gives me a "could not find error".
> 
>> assignChromosomeRegion(peaks.RD=rda.dRF8,exon=Exon,TSS=TSS,utr5=utr5,utr3=utr
>> 3,proximal.promoter.cutoff=1000,immediate.downstream.cutoff=1000)
> Error: could not find function "assignChromosomeRegion"
> 
> Below I've listed my libraries, so that you can see what I have loaded in R
> (2.15). I'm running R in Rstudio (0.97.332). Although the function isn't
> found, when I enter by hand: "assignChromosomeRegion(" and hit tab, it does
> give me the parameter options for the function assignChromosomeRegion. But
> when I execute, it says it couldn't find the function. Can you help?
> Thank you and Best wishes,
> 
> - Stefan.
> 
> 
> Packages in library
> Œ/Library/Frameworks/R.framework/Versions/2.15/Resources/library¹:
> 
> AnnotationDbi                 Annotation Database Interface
> base                          The R Base Package
> Biobase                       Biobase: Base functions for Bioconductor
> BiocGenerics                  Generic functions for Bioconductor
> BiocInstaller                 Install/Update Bioconductor and CRAN Packages
> biomaRt                       Interface to BioMart databases (e.g. Ensembl,
> COSMIC
>                               ,Wormbase and Gramene)
> Biostrings                    String objects representing biological
> sequences, and
>                               matching algorithms
> bitops                        Functions for Bitwise operations
> boot                          Bootstrap Functions (originally by Angelo Canty
> for S)
> BSgenome                      Infrastructure for Biostrings-based genome data
> packages
> BSgenome.Ecoli.NCBI.20080805
>                               Escherichia coli full genomes
> caTools                       Tools: moving window statistics, GIF, Base64,
> ROC AUC, etc.
> ChIPpeakAnno                  Batch annotation of the peaks identified from
> either
>                               ChIP-seq, ChIP-chip experiments or any
> experiments resulted
>                               in large number of chromosome ranges.
> class                         Functions for Classification
> cluster                       Cluster Analysis Extended Rousseeuw et al.
> codetools                     Code Analysis Tools for R
> colorspace                    Color Space Manipulation
> compiler                      The R Compiler Package
> datasets                      The R Datasets Package
> DBI                           R Database Interface
> dichromat                     Color Schemes for Dichromats
> digest                        Create cryptographic hash digests of R objects
> foreign                       Read Data Stored by Minitab, S, SAS, SPSS,
> Stata, Systat,
>                               dBase, ...
> gdata                         Various R programming tools for data
> manipulation
> GenomicRanges                 Representation and manipulation of genomic
> intervals
> ggplot2                       An implementation of the Grammar of Graphics
> GO.db                         A set of annotation maps describing the entire
> Gene
>                               Ontology
> gplots                        Various R programming tools for plotting data
> graphics                      The R Graphics Package
> grDevices                     The R Graphics Devices and Support for Colours
> and Fonts
> grid                          The Grid Graphics Package
> gtable                        Arrange grobs in tables.
> gtools                        Various R programming tools
> IRanges                       Infrastructure for manipulating intervals on
> sequences
> KernSmooth                    Functions for kernel smoothing for Wand & Jones
> (1995)
> labeling                      Axis Labeling
> lattice                       Lattice Graphics
> limma                         Linear Models for Microarray Data
> MASS                          Support Functions and Datasets for Venables and
> Ripley's
>                               MASS
> Matrix                        Sparse and Dense Matrix Classes and Methods
> methods                       Formal Methods and Classes
> mgcv                          Mixed GAM Computation Vehicle with GCV/AIC/REML
> smoothness
>                               estimation
> multtest                      Resampling-based multiple hypothesis testing
> munsell                       Munsell colour system
> nlme                          Linear and Nonlinear Mixed Effects Models
> nnet                          Feed-forward Neural Networks and Multinomial
> Log-Linear
>                               Models
> org.Hs.eg.db                  Genome wide annotation for Human
> parallel                      Support for Parallel computation in R
> plyr                          Tools for splitting, applying and combining data
> proto                         Prototype object-based programming
> RColorBrewer                  ColorBrewer palettes
> RCurl                         General network (HTTP/FTP/...) client interface
> for R
> reshape2                      Flexibly reshape data: a reboot of the reshape
> package.
> rpart                         Recursive Partitioning
> RSQLite                       SQLite interface for R
> scales                        Scale functions for graphics.
> spatial                       Functions for Kriging and Point Pattern Analysis
> splines                       Regression Spline Functions and Classes
> stats                         The R Stats Package
> stats4                        Statistical Functions using S4 Classes
> stringr                       Make it easier to work with strings.
> survival                      Survival Analysis
> tcltk                         Tcl/Tk Interface
> tools                         Tools for Package Development
> utils                         The R Utils Package
> VennDiagram                   Generate high-resolution Venn and Euler plots
> XML                           Tools for parsing and generating XML within R
> and S-Plus.
> 
> Packages in library Œ/Applications/RStudio.app/Contents/Resources/R/library¹:
> 
> manipulate                    Interactive Plots for RStudio
> rstudio                       Tools and Utilities for RStudio