parse.headers: Convenience function to parse metadata from sequence headers

In PoonLab/clustuneR: Molecular clustering implementation and predictive optimization

Convenience function to parse metadata from sequence headers

Description

Translates a set of sequence headers into a data.frame object for data input. Requires that every sequence header contains the same number and type of values, separated by a reserved delimiter character, e.g., underscore "_"

Usage

parse.headers(
  headers,
  var.names = c(),
  var.transformations = list(),
  sep = "_"
)

Arguments

headers:	character, vector of sequence names such as obtained by names(x) where x is an ape::DNAbin object.
var.names:	character, The names of the variables represented in each header.
var.transformations:	list, A list of transformation functions (such as as.Date()) these transform each row into it's proper type. By default, each value is taken literally (i.e., as.character).
sep:	character, The separator character that splits up the headers into values.

Value

A data.table object containing sequence meta data paired to headers. See seq.info.ex, for more details and an example

Examples

seq.info <- parse.headers(names(alignment.ex), var.names = c("ID", "CollectionDate", "Subtype"),
                         var.transformations = list(as.character, as.Date, as.factor))

PoonLab/clustuneR documentation built on Jan. 29, 2024, 2:40 a.m.