read_ref: Load a reference map

In dmuijen/mapfuser: Construct Consensus Genetic Maps and Estimate Recombination Rates

Description

Read a reference map, either a reference genetic map or a map with physical genome positions

Usage

read_ref(MF.obj = NULL, ref_file = ref_file, sep = NULL, header = TRUE,
  na.strings = "NA", type = c("delim", "JoinMap"))

Arguments

MF.obj	A mapfuser object
ref_file	path to reference file
sep	The field separator character, see read.delim
header	A logical value indicating whether the files contains the names of variable int the first line, see read.delim()
na.strings	How to interpret missing values? See read.delim
type	Type of input data, either delimited file with columns "Marker", "LG", and "Position" or a JoinMap ".map" file.

Value

A mapfuser object with the reference map loaded to the ref_map slot. Name of the reference map is saved to the config.

Author(s)

Dennis van Muijen

Examples

fpath <- system.file("extdata", package="mapfuser")
maps <- list.files(fpath, pattern = "Col", full.names = TRUE)
MF.obj <- read_maps(mapfiles = maps, sep = ",", header = TRUE,
mapweights = rep(1,7), type = "delim")
ref_file <- list.files(fpath, pattern = "reference", full.names = TRUE)
MF.obj <- read_ref(MF.obj = MF.obj, ref_file = ref_file, sep = ",",
header = TRUE, na.string = NA, type = "delim")

dmuijen/mapfuser documentation built on May 28, 2019, 7:53 p.m.