Dear All,

I experience the following problem when trying to extract reads from bam
files using Rsamtools on 1000 genomes hapmap BAM file. Would be grateful
for your help, thanks.

Sergey

 

 

########

 

 

w=GRanges(seqnames = "1",ranges = IRanges(1000,width=400))

p2 <- ScanBamParam(which=w)

res2 <- scanBam("NA12878.SLX.maq.SRP000031.2009_08.bam",p2)

 

 

Error in as.character.default(x) :   no method for coercing this S4
class to a vector

 

 

> sessionInfo()

R version 2.10.1 (2009-12-14)

x86_64-unknown-linux-gnu

 

locale:

 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C

 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8

 [5] LC_MONETARY=C              LC_MESSAGES=en_GB.UTF-8

 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C

 [9] LC_ADDRESS=C               LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

 

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base

 

other attached packages:

[1] Rsamtools_1.0.5     Biostrings_2.16.6   GenomicRanges_1.0.4

[4] IRanges_1.6.8

 

loaded via a namespace (and not attached):

[1] Biobase_2.6.1

 
  
----------------------------------------------
Sergii Ivakhno

PhD student

Computational Biology Group
Cancer Research UK Cambridge Research Institute
Li Ka Shing Centre
Robinson Way
Cambridge CB2 0RE
England

+44 (0)1223 404293 (O)
+44 (0)1223 404128 (F)

http://www.compbio.group.cam.ac.uk <http://www.compbio.group.cam.ac.uk/>
/


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