[Seqinr-forum] HELP for using R for codon usage data analysis

[Kinshuk Nayak]

Sir,
I am a student in bioinformaics.I am interested to use R 2.14.1 for codon usage analysis like example given at http://pbil.univ-lyon1.fr/datasets/charif04/. Here the example is customised for three genomes.I would like to run it for my sequence data/ genome. I have filtered set of sequences having length >300bp and stored in fasta format(mygenome1.fasta)  in the folder in which R2.14.1 is installed. I have edited R script as follows.But it is showing error message during running the script.Could you please check and correct it.

SCRIPT

library(ade4)
library(seqinr)

sessionInfo()

mygenome1 <-read.fasta("mygenome1.fasta",seqonly=T)                  
seqmygenome1 <- lapply(mygenome1$req, getSequence)
####################################################################
#
# From sequences, build dataframes with codon usage for each sequence. 
#
####################################################################
mkdata <- function(seqs)
{
  tab <- sapply(seqs, uco)  
  tab <- as.data.frame(tab)
  return( tab )
}
tabmygenome1 <- mkdata(seqmygenome1)
####################################################################
#
# Run correspondence analysis on merged dataset:
#
####################################################################
tab <- cbind(tabmygenome1)
names(tab) <- 1:ncol(tab)
coa <- dudi.coa(tab, scan = FALSE, nf = 2)
####################################################################
#
# Run synonymous codon usage analysis:
#
####################################################################
facaa <- as.factor(aaa(translate(sapply(rownames(tab),s2c))))
scua <- wca(coa, facaa, scan = FALSE, nf = 2)
####################################################################
#
# Plot first factorial map:
#
####################################################################
facsp <- as.factor(rep(c("mygenome1"),
                       c(ncol(tabmygenome1)))
s.class(scua$co, fac = facsp, cstar = 0, label = "",
        col = c("green"), cell=0, cpoint=0.8,
        sub="First factorial map for synonymous codon usage in Tri-Tryp")
s.label(scua$li, add.plot = TRUE, clab = 0.75)
legend( x = 0.1, y = -0.4, pch = 19, col = c("green"), 
       legend = c(expression(italic("mygenome1")),
                  
       xjust = 0, cex = 0.8)
####################################################################
#
# END
#
####################################################################
 
AFTER RUNNING

 > library(ade4)
Attaching package: ‘ade4’
The following object(s) are masked from ‘package:base’:
    within
> library(seqinr)
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    
attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] seqinr_3.0-6 ade4_1.4-17 
> mygenome1 <-read.fasta("mygenome1.fasta",seqonly=T) 
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file 'mygenome1.fasta': No such file or directory



Thanking you
Kinshuk Chandra Nayak
Lab. Tech & In-Charge IPR Cell
Institute of Life Sciences
Department of Biotechnology,Govt India
Bhubaneswar-751023,
India
Ph-0674-2300137,2301460,2301476,2301219 (EXTN:279)
Mail: 
kinshuk at ils.res.in
kinshukils at hotmail.com
kinshuk_nayak at yahoo.co.in
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