CleanSeqs: Removes sites that contain a certain percentage of missing...

In bomeara/sleq: sleq

Description

Removes sites that contain a certain percentage of missing data across taxa

Usage

CleanSeqs(seq, seq.type = "dna", cutoff = 0.5)

Arguments

seq	A character matrix or seqalignment object
seq.type	The type of sequences contained in the alignment.
cutoff	The proportion of non-ambiguous data present to trim from the alignment.

Examples

## Not run: 
test.sequences <- read.alignment(file = system.file("sequences/test.phylip",
package = "seqinr"), format = "phylip")
test.sequences.clean <- CleanSeqs(test.sequences, seq.type="dna", cutoff=0.5)
test.sequences <- as.matrix(read.alignment(file = system.file("sequences/test.phylip",
package = "seqinr"), format = "phylip"))
test.sequences.clean <- CleanSeqs(test.sequences, seq.type="dna", cutoff=0.5)

## End(Not run)

bomeara/sleq documentation built on May 12, 2019, 11:36 p.m.