getCodonFeatures-methods: Index genome according to provided exons

Description Usage Arguments Value

Description

Author: Christopher Ward
Index genome according to codon positions in coding sequence.
This can be useful when downstream analysis or output of alignements should only be applied to certain codons.
For example calculating genetic Tajima's D on only 4-fold sites or outputting fasta files based on codon position.

Usage

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getCodonFeatures(genome, exons, nCores = 1, position = "all",
  fourFoldCodon = "include", ...)

Arguments

genome

character or DNAStringSet
Import fasta reference genome from file by passsing a character or provide a preloaded (using Biostrings::readDNAStringSet()) DNAStringSet

exons

GrangesList
Generated using getFeatures() by passing "gene:cds" to the feature argument.

nCores

numeric Number of cores allcated.

position

character Options are "all", default, or any combination of c("first", "second", "third").
Output will contain only specified codon positions.

fourFoldCodon

character Options are NULL, "only" or "remove".
Determines what to do with 4-fold degenerate sites.

NULL, the default, will have no effect on the output, "only" will include only 4 fold degenerate sites in the output,
"exclude" will output all sites (unless a position is specified) excluding 4-fold degenerate sites.

"only" is incompatable with specifying a position.

Value

An object of class GRanges containing codon ranges for positions specified.


CMWbio/geaR documentation built on June 21, 2019, 10:48 a.m.