[BioC] ChIPpeakAnno

[Zhu, Lihua (Julie)]

Dear Takele,

Here is some code snippet and documentation that might be useful to you.

### assuming your dataset has a header column
x <- read.table(yourdataset, sep="\t", header=TRUE, stringsAsFactors=FALSE)
### convert x to RangedData or GenomicRanges
myexp = RangedData(IRanges(start= as.numeric(x[,2]), end=as.numeric(x[,3]),
names=rownames(x)), space= x[,1])

Then use getAnnotation to obtain gene annotation of your choice, e.g.,
chicken. For details on how to use getAnnotation, please type ?getAnnotation
in a R console.

If you have already downloaded the gene annotation in a bed or gff file,
then you can use function BED2RangedData or GFF2RangedData
to create annotation. For details on how to use these functions, please type
?BED2RangedData or ?GFF2RangedData in a R console.

Finally, use annotatePeakInBatch to annotate your dataset with the
annotation you obtained.

AnnotatedDataset <- AnnotatePeakInBatch(myexp,
AnnotationData=YourAnnotation)
For detailed parameter setting, please type ?annotatePeakInBatch in a R
console.

Here is the user guide, publication and workshop materials on ChIPpeakAnno.
http://www.bioconductor.org/packages/release/bioc/vignettes/ChIPpeakAnno/ins
t/doc/ChIPpeakAnno.pdf
http://www.biomedcentral.com/content/pdf/1471-2105-11-237.pdf
http://www.bioconductor.org/help/course-materials/2011/BioC2011/LabStuff/ChI
PpeakAnno-BioC2011.pdf

Could you please cc bioconductor list for future correspondence so others
can contribute or benefit? Thanks!

Hope this is useful.

Best regards,

Julie


*******************************************
Lihua Julie Zhu, Ph.D
Research Associate Professor
Program in Gene Function and Expression
Program in Bioinformatics and Integrative Biology
Program in Molecular Medicine
University of Massachusetts Medical School
364 Plantation Street, Room 613
Worcester, MA 01605
508-856-5256
http://profiles.umassmed.edu/profiles/ProfileDetails.aspx?From=SE&Person=113
4


On 8/20/14 4:59 AM, "Takele Desta" <plxtd at nottingham.ac.uk> wrote:

> Dear Zhu
> 
> I have a data set containing three columns. Column 1 is chromosome, and column
> 2 & 3  indicate the start and end position ( bp) of the region I'm interested
> in. I want to map genes that found (1) within and (2) within and around this
> region. I'm working on chicken using HD (600K) SNP array. How I can use your
> package to accomplish this task?
> 
> Best regards,

> 
>