ChIPpeakAnno
0
0
Entering edit mode
Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 10 weeks ago
United States
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/ChIPpeakAn no/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&Pers on=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, > >
SNP Annotation annotate convert SNP Annotation annotate convert • 893 views
ADD COMMENT

Login before adding your answer.

Traffic: 174 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6