[BioC] rho statistics for dinucleotide abundance from a sequence file

[Utpal Bakshi [guest]]

Hi all, 

I have a sequence file (fasta format) and want to calculate the rho statistics for dinucleotide abundance value on my data.. the code which I use is (using seqinr library and current working directory) 

seq_info<-read.fasta("gene.txt") 
rho(seq_info[1],2) 

but it yields only the dinucleotides, not their rho values, i.e, 

> rho(seq_info[1],2) 
aa ac ag at ca cc cg ct ga gc gg gt ta tc tg tt 

I will be grateful if anyone solve this.. I've also attached the sequence below.. 
Thanks in advance.. 
 


>gi|270279749|gene0003
ATGTATATGAGAAAGGAAGAGCCTAGCGGCTCAGACAAGATTATGACTTCAGTTGTTGTTGTAGGTACCCAATGGGGCGATGAAGGTAAAGGGAAAATTACAGATTTTCTTTCAGCTAATGCAGAGGTGATTGCTCGTTACCAAGGTGGTGATAATGCTGGTCACACAATTGTGATTGATGGCAAGAAATTTAAGTTGCACTTGATTCCATCTGGAATTTTCTTCCCTGAAAAAATTTCAGTTATTGGAAACGGTATGGTTGTAAACCCTAAATCACTTGTGAAAGAATTGTCTTATCTGCATGAAGAAGGTGTTACAACAGATAATCTACGTATCTCTGATCGTGCGCATGTTATTTTGCCTTACCACATTGAGTTGGATCGCTTGCAAGAAGAAGCTAAGGGTGATAATAAGATTGGTACTACAATAAAGGGAATTGGTCCAGCATATATGGACAAAGCTGCTCGTGTCGGGATTCGTATTGCAGATCTTTTGGATAAGGATATTTTCCGTGAACGCTTGGAACGCAATCTTGCGGAGAAGAATCGTCTGTTTGAAAAATTGTATGACAGTACTCCTATTTCAATTGATGATATTTTTGAAGAGTACTATGAGTATGGCCAACAAATTAAGCAGTATGTGACAGATACATCTGTTATTTTGAACGATGCGCTTGATAACGGCAAACGTGTGCTTTTTGAAGGTGCGCAAGGTGTCATGTTGGATATTGACCAAGGTACTTATCCATTTGTTACTTCTTCAAACCCTGTTGCTGGTGGTGTGACAATTGGGTCTGGTGTTGGTCCAAGTAAGATTGACAAGGTTGTAGGTGTTTGTAAAGCCTATACAAGTCGTGTAGGTGATGGACCTTTCCCAACTGAATTATTTGATGAAGTGGGAGATCGCATTCGTGAAGTAGGTCATGAGTATGGTACAACAACTGGCCGTCCACGTCGTGTGGGTTGGTTTGACTCAGTTGTGATGCGTCAC
 AGCCGTCGTGTATCTGGTATTACCAATCTTTCATTGAACTCTATCGATGTTTTGAGCGGTTTGGATACTGTGAAAATCTGTGTGGCCTATGATCTCGATGGTCAACGTATCGACCACTACCCAGCTAGTCTTGAACAGTTGAAACGTTGCAAACCTATCTACGAAGAATTGCCAGGGTGGTCAGAAGACATCACAGGAGTTCGTAATTTGGAAGATCTTCCTGAGAATGCGCGTAACTATGTTCGTCGTGTGAGTGAATTGGTTGGCGTTCGTATTTCGACATTCTCAGTAGGTCCTGGTCGTGAACAAACCAATATTTTAGAAAGTGTTTGGTCTTAA

 -- output of sessionInfo(): 

R version 2.14.0 (2011-10-31)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252   
[3] LC_MONETARY=English_India.1252 LC_NUMERIC=C                  
[5] LC_TIME=English_India.1252    

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

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