Question: assignChromosomeRegion in 2.6.0 ChIPpeakAnno

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Julie Zhu •

**4.0k**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=utr
5,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
> ?/Library/Frameworks/R.framework/Versions/2.15/Resources/library?:
>
> 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
?/Applications/RStudio.app/Contents/Resources/R/library?:
>
> manipulate Interactive Plots for RStudio
> rstudio Tools and Utilities for RStudio