[BioC] How can I obtain gene name from chromosome location?

[Yoo, Seungyeul]

Hi all,

I'm working on DNA-methylation data of Lung Genomes.

I'm using CHARM packages for the analysis of differentially methylated regions.

I can have a list of chromosomal locations indicating genes but I don't know how I map this location into specific gene names.

> head(pns)               
[1] "chr19:4205395-4220723"   "chr16:73793547-73835933"
[3] "chr22:18115791-18146966" "chr19:60540822-60563218"
[5] "chr16:14630202-14638324" "chr19:49197954-49200178"

Because I also have gene expression dataset, I want to integrate dna methylation data so obtaining genename is very critical.

Please let me have any advices.

Best regards,

Seungyeul 

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] gplots_2.11.0                      MASS_7.3-17                       
 [3] KernSmooth_2.23-7                  caTools_1.13                      
 [5] bitops_1.0-4.1                     gdata_2.11.0                      
 [7] gtools_2.7.0                       BSgenome.Hsapiens.UCSC.hg18_1.3.17
 [9] BSgenome_1.24.0                    Biostrings_2.24.1                 
[11] GenomicRanges_1.8.7                IRanges_1.14.3                    
[13] pd.feinberg.hg18.me.hx1_0.99.2     oligo_1.20.3                      
[15] oligoClasses_1.18.0                RSQLite_0.11.1                    
[17] DBI_0.2-5                          charm_2.2.0                       
[19] genefilter_1.38.0                  RColorBrewer_1.0-5                
[21] fields_6.6.3                       spam_0.29-1                       
[23] SQN_1.0.4                          nor1mix_1.1-3                     
[25] mclust_3.4.11                      Biobase_2.16.0                    
[27] BiocGenerics_0.2.0                

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.18.1  BiocInstaller_1.4.7   affxparser_1.28.0    
 [4] affyio_1.24.0         annotate_1.34.0       bit_1.1-8            
 [7] codetools_0.2-8       ff_2.2-7              foreach_1.4.0        
[10] iterators_1.0.6       limma_3.12.1          multtest_2.12.0      
[13] parallel_2.15.0       preprocessCore_1.18.0 siggenes_1.30.0      
[16] splines_2.15.0        stats4_2.15.0         survival_2.36-12     
[19] sva_3.2.1             xtable_1.7-0          zlibbioc_1.2.0