How to create a chromosome location map by locus ID
Sake <tlep.nav.ekas at hccnet.nl> writes:
Neil Shephard wrote:
Whats wrong with things like the HapMap Genome Browser that allows you to zoom in and out and to produce customised annotations of chromosomal regions at varying resolutions (see http://www.hapmap.org/)? Of course I'm assuming that you are looking at human chromosomes ;-) If not then perhaps the UCSC Genome Browser may be of use as it has a large number genomes you can browse (see http://genome.ucsc.edu/cgi-bin/hgGateway ). If you really want to do this in R You might get some mileage out of the lodplot package which can draw ideograms (which is what a schematic of a choromsome with bandings from different stainings is called), although the dataset available for it is again for human chromosomes (see http://cran.r-project.org/web/packages/lodplot/index.html ). Perhaps worth checking out the Genetics Task View too thats linked from CRAN. Neil
I'm well known with all the tools on the internet which allow you to find the position of genes on a chromosome. The only thing is, none of them has the function to upload a list of e.g. 300 genes. I have a list of over expressed genes, and I want to know on which chromosome they are so I can see if there is some kind of link between the genes and the position on a chromosome. I already have made a list of the locus of each gene, but now I want to make some sort of plot that allows me to visualise where the genes are located. So the reason I don't use those webtools is because I have 300 genes and I'm not planning to search for each gene individual.
There are many tools in the R / Bioconductor project that address these types of issues; a typical use case might use one of the 'org' packages, e.g., org.Hs.eg.db though there are many others, to extract information or to map between inforamtion types.
library(org.Hs.eg.db) ls(2)
[snip]
toTable(org.Hs.egCHRLOC[c('1000', '10000')])
gene_id start_location Chromosome 1 1000 -23784933 18 2 10000 -241718157 1 3 10000 -241733106 1
toTable(org.Hs.egSYMBOL[c('1000', '10000')])
gene_id symbol 1 1000 CDH2 2 10000 AKT3 There are a number of packages for displaying this information, but usually in conjunction with additional covariates. GenomeGraphs provides really pretty pictures (though is more for detailed presentation of individual genes). rtracklayer is an interface that lets you lay and navigate tracks on web-based genome browsers. The place to start with Bioconductor is http://bioconductor.org, e.g., basic install: http://bioconductor.org/docs/install/ package list: http://bioconductor.org/packages/release/Software.html
source('http://bioconductor.org/biocLite.R')
biocLite() # default packages
biocLite('org.Hs.eg.db') # specific package
library(org.Hs.eg.db)
Look to the AnnotationDbi 'vignettes', either on-line (link to the AnnotationDbi package page from the list above) or in the package itself (via openVignettes()). Any follow-up questions about Bioconductor should go to the Bioconductor mailing list http://bioconductor.org/docs/mailList.html Martin
The lodplot package looks promising (already found it;-), but thanx anyway!), but I did not yet figured out how to use it properly. I've not found any tutorial or example data to test it. -- View this message in context: http://www.nabble.com/How-to-create-a-chromosome-location-map-by-locus-ID-tp21474206p21497719.html Sent from the R help mailing list archive at Nabble.com.
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793