[BioC] merging GRange objects

Murli [guest] guest at bioconductor.org
Tue Jun 25 01:55:28 CEST 2013


I would appreciate if you could tell me if the way I am merging the GappedAlignments object and GRanges objects is correct. mate1 and mate2 are GappedAlignment objects. I am merging them in order to associate my reads with the annotation. 

txdb = TxDb.Hsapiens.UCSC.hg19.knownGene

mate.range= GRanges(seqnames(mate1[isSameCzome]),IRanges(start(mate1[isSameCzome])-offset,start(mate1[isSameCzome])+offset))

codingRegions = refLocsToLocalLocs(mate.range, txdb)

trans.info=select(txdb, key=values(codingRegions)$TXID, cols=c("GENEID","TXNAME"), keytype="TXID")

trans.names=select(org.Hs.eg.db, trans.info$GENEID, c("GENENAME", "SYMBOL"))

mrg.data1=merge(as.data.frame(trans.names), as.data.frame(trans.info), by.x="ENTREZID", by.y="GENEID")

mrg.data2=merge(mrg.data1, as.data.frame(codingRegions), by.x="TXID", by.y="TXID")

Thanks ../Murli

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-redhat-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
 [1] biomaRt_2.16.0                         
 [2] org.Hs.eg.db_2.9.0                     
 [3] RSQLite_0.11.4                         
 [4] DBI_0.2-7                              
 [5] VariantAnnotation_1.6.6                
 [6] Rsamtools_1.12.3                       
 [7] BSgenome.Hsapiens.UCSC.hg19_1.3.19     
 [8] BSgenome_1.28.0                        
 [9] Biostrings_2.28.0                      
[10] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2
[11] GenomicFeatures_1.12.2                 
[12] AnnotationDbi_1.22.6                   
[13] Biobase_2.20.0                         
[14] GenomicRanges_1.12.4                   
[15] IRanges_1.18.1                         
[16] BiocGenerics_0.6.0                     

loaded via a namespace (and not attached):
[1] bitops_1.0-5       RCurl_1.95-4.1     rtracklayer_1.20.2 stats4_3.0.1      
[5] tcltk_3.0.1        tools_3.0.1        XML_3.98-1.1       zlibbioc_1.6.0

Sent via the guest posting facility at bioconductor.org.

More information about the Bioconductor mailing list