base.freq.msa: Get the frequencies of characters in an alignment
In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description Usage Arguments Value Author(s) See Also

Get the frequencies of characters in an alignment

1	base.freq.msa(x, seq = NULL, ignore.missing = TRUE, ignore.gaps = TRUE)

`x`	An object of type `msa`
`seq`	A vector of character strings identifying the sequence(s) to get base frequencies for. If `NULL`, use all sequences.
`ignore.missing`	If TRUE, ignore missing data characters ("N" and "?"). Must be TRUE if seq is stored as a pointer.
`ignore.gaps`	If TRUE, ignore gaps. Must be TRUE if seq is stored as a pointer.

A data frame with one row for each unique state (usually "A", "C", "G", "T", and possibly "N", "?", "-", counts for each state, and overall frequency of each state.

Melissa J. Hubisz

statfreq.msa, which gets observed frequencies of states in an alignment with respect to a substitution model, and works for pointers.

rphast documentation built on May 1, 2019, 9:26 p.m.