[BioC] assignChromosomeRegion in 2.6.0 ChIPpeakAnno
Zhu, Lihua (Julie)
Julie.Zhu at umassmed.edu
Fri Mar 15 01:50:51 CET 2013
Stefan,
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!
ChIPpeakAnno:::assignChromosomeRegion
Best regards,
Julie
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".
>>
>>>
assignChromosomeRegion(peaks.RD=rda.dRF8,exon=Exon,TSS=TSS,utr5=utr5,utr3=ut>>>
r
>>> 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
>
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