msa: MSA Objects
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Details Author(s) Examples

Creates a new MSA object given sequences.

1 2	msa(seqs, names = NULL, alphabet = "ACGT", is.ordered = TRUE, offset = NULL, pointer.only = FALSE)

`seqs`	a character vector containing sequences, one per sample
`names`	a character vector identifying the sample name for each sequence. If `NULL`, use "seq1", "seq2", ...
`alphabet`	a character string containing valid non-missing character states
`is.ordered`	a logical indicating whether the alignment columns are stored in order. If NULL, assume columns are ordered.
`offset`	an integer giving the offset of coordinates for the reference sequence from the beginning of the chromosome. The reference sequence is assumed to be the first sequence. Not used if is.ordered==FALSE.
`pointer.only`	a boolean indicating whether returned alignment object should be stored by reference (see Details)

Make a new multiple sequence alignment (MSA) object given a vector of character strings. They can be optionally annotated with sample names.

Each character string in seqs must be the same length, and number of elements in names (if provided) must match the number of elements in seqs.

Alphabet generally does not have to be specified if working with DNA alignments.

About storing objects as pointers: If pointer.only==FALSE, the MSA object will be stored in R and can be viewed and modified by base R code as well as RPHAST functions. Setting pointer.only=TRUE will cause the object to be stored by reference, as an external pointer to an object created by C code. This may be necessary to improve performance, but the object can then only be viewed/manipulated via RPHAST functions. Furthermore, if an object is stored as a pointer, then its value is liable to be changed when passed as an argument to a function. All RPHAST functions which change the value of an external pointer make a note of this in the help pages for that function. For example, extract.feature.msa will alter an alignment if it is passed in as an external pointer (the argument will be changed into the return value). If this is undesireable, the copy.msa function can be used: extract.feature.msa(copy.msa(align)) will preserve the original alignment. Simple copying, ie, align2->align1 of objects stored as pointer will not behave like normal R objects: both objects will point to the same C structure, and both will be changed if either one is altered. Instead align2 <- copy.msa(align1) should be used.

Melissa J. Hubisz and Adam Siepel

# Here is an MSA object stored in the default mode
m1 <- msa(seqs=c("ACGTAT", "AGGTAA", "AGGTAG"),
          names=c("human", "mouse", "rat"))
m2 <- m1
# NOTE seqs would not be directly accessible if stored by reference
m2$seqs[3] <- "AAAAAA"
print(m1)
print(m1, print.seq=TRUE)
print(m2, print.seq=TRUE)