readAnnotationFile: Read an annotation file

In wrightrc/r1001genomes: Access and analyze the 1001 genomes Arabidopsis resequencing dataset

Description

Read an annotation file

Usage

readAnnotationFile(filename, wide = FALSE, domains = TRUE,
  gene_info = NULL)

Arguments

filename	filename or path to the annotation csv file to be read. This should by default be a long format csv containing at least columns named "gene", "annotation", "annotation_type", "position", and "position_type". "Gene" should match the names of the tracks you wish to annotate. "Annotation" is a description of the position and may be the start or end of annotations spanning multiple consecutive positions (multiposition annotations) (e.g. domain_start), note that the underscore separator and "start" and "end" are crucial to the processing of domain annotations and "start" and "end" should not be used in single position annotations. "Position_type" should be either "AA" refering to the amino acid position, or "DNA" refering to the coding sequence.
wide	is the annotation file a wide format data frame with colums for the start and end of each domain? Defaults to FALSE
domains	create multiposition annotations from annotations containing "start" and "end"? This will allow shading of the entire domain as opposed to just marking the start and end positions.

Value

returns an annotation data frame, or if domains = TRUE a list of data frames with the first "domains" element containing multiposition annotation and the second "positions" element containing single position annotations.

Examples

readAnnotationFile(filename = system.file("extdata", "AFB_annotations.csv",
                                        package = "r1001genomes"))

wrightrc/r1001genomes documentation built on Nov. 10, 2019, 12:45 p.m.