sample.msa: Sample columns from an MSA
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Value Note Author(s) Examples

Sample columns from an MSA

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## S3 method for class 'msa'
sample(x, size, replace = FALSE, prob = NULL,
  pointer.only = FALSE)

`x`	An object of type `msa`
`size`	The number of columns to sample
`replace`	Whether to sample with replacement
`prob`	A vector of probability weights for sampling each column; `prob=NULL` implies equal probability for all columns. Probabilities need not sum to one but should be non-negative and can not all be zero.
`pointer.only`	If `TRUE`, return only a pointer to an alignment object stored in C (useful for large objects; advanced use only).

An object of type msa with columns randomly re-sampled from the original

This function is implemented using R's sample function in conjunction with "[.msa". It will not alter the value of x even if it is stored as a pointer.

Melissa J. Hubisz and Adam Siepel

m <- msa(seqs=c("AAAAAAAAAACCCCCGGT", "GGGGGGGGGGTTTTTCCA", "CCCCCCCCCCAAAAAGGA"),
         names=c("human", "mouse", "rat"))
sample.msa(m, 10, replace=TRUE)
sample.msa(m, 10, replace=TRUE, prob=c(rep(1, 10), rep(2, 5), rep(5, 2), 10))