square-bracket-assign-msa: Replace subsets of an alignment
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Value Note Author(s) Examples

Replace subsets of an alignment

1 2	## S3 replacement method for class 'msa' x[rows, cols] <- value

`x`	An object of type `msa`
`rows`	A numeric vector of sequence indices, character vector (containing sequence names), or logical vector. If logical vector, it will be recycled as necessary to the length of `nrow.msa(x)`. If not provided, all rows are selected.
`cols`	A numeric vector of alignment columns, or a logical vector. If logical vector it will be recycled to the same length as `ncol.msa(x)`. Note that these are coordinates with respect to the entire alignment. x$idx.offset is ignored here. If cols is not provided, all columns are selected.
`value`	The value to replace in the indicated rows/columns. Should be a character representing a base (ie, "A", "C", "G", "T", "N", "-"). Can be a single value or a vector of values which match number of selected cells. This value will be recycled to the necessary length, and an error produced if the necessary length is not an even multiple of `length(value)`. Can also give a single character string, in which case it will be expanded into a vector using `strsplit`.

An object of type msa with the chosen rows/columns replaced by value.

If x is stored as a pointer, x will be changed to the return value.

Melissa J. Hubisz

m <- msa(seqs=c("ACGTAT", "AGGTAA", "AGGTAG"),
         names=c("human", "mouse", "rat"))
m[1:2,4:6] <- "G"
m[1,] <- "A"
m[,4:5] <- "-"
m["rat",] <- "ABCDEF"