[BioC] readRNAMultipleAlignmen - filepath

KoRR [guest] guest at bioconductor.org
Sun Aug 24 17:07:59 CEST 2014

I am not quite understand the way to specify the filepath in "readRNAMultipleAlignmen" function.  

Step 1: I try to read the file(Testing13Seq.aln) by specify the true path of my file, but it result in error(origMAlign1). 

Step 2: I move my file to the exdata folder in the Biostring package, but I still tried to read the data with the true path. Again it result in error(origMAlign2).

Step 3: The data remain at exactly the same path as in Step 2. Rather call the the file with fullpath, I call through "system.file" function. Now the data can be read (origMAlign3).

However, the pathfile in Step 2 and Step 3 are exactly the same path. So my question is, do I need to move my data to the BioString package everytime I need to read it, then call the file via system.file function. Why cant I just type the fullpath, then read the file?

 -- output of sessionInfo(): 

> origMAlign1 <- readRNAMultipleAlignment("D:/Research/Chivalai/DENGUE/Data/FASTA/Testing13Seq.aln",format="clustal")
Error in .Call2("new_XStringSet_from_CHARACTER", ans_class, ans_elementType,  : 
  key 84 (char 'T') not in lookup table

> origMAlign2 <- readRNAMultipleAlignment(filepath ="C:/Users/C. Temiyasathit/Documents/R/win-library/3.1/Biostrings/extdata/Testing13Seq.aln",format="clustal")
Error in .Call2("new_XStringSet_from_CHARACTER", ans_class, ans_elementType,  : 
  key 84 (char 'T') not in lookup table

> origMAlign3 <- readDNAMultipleAlignment(filepath =system.file("extdata","Testing13Seq.aln",package="Biostrings"),format="clustal")
> origMAlign3
DNAMultipleAlignment with 13 rows and 11239 columns    aln                                                                              names               
 [1] ---------------------------------------...-------------------------------------- gi|31339329|gb|AB...
[13] AGTTGTTAGTCTGTGTGGACCGACAAGGACAGTTCCGAA...-------------------------------------- gi|148828520|gb|E...

> filepath =system.file("extdata","Testing13Seq.aln",package="Biostrings")
> filepath
[1] "C:/Users/C. Temiyasathit/Documents/R/win-library/3.1/Biostrings/extdata/Testing13Seq.aln"

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