[BioC] assignChromosomeRegion in 2.6.0 ChIPpeakAnno

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Fri Mar 15 01:50:51 CET 2013


Thanks for reporting this! Actually the function assignChromosomeRegion  is
not exported.

Could you please try the following to see if you can use it? Thanks!


Best regards,


On 3/14/13 7:36 PM, "Lihua Julie Zhu" <julie.zhu at umassmed.edu> wrote:

> 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".
>>> 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,
>>                               ,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
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor

More information about the Bioconductor mailing list