createTetraOriginInput {polymapR}

Create input files for TetraOrigin using an integrated linkage map list and marker dosage matrix

Description

createTetraOriginInput is a function for creating an input file for TetraOrigin, combining map positions with marker dosages.

Usage

createTetraOriginInput(
  maplist,
  dosage_matrix,
  bin_size = NULL,
  bounds = NULL,
  remove_markers = NULL,
  outdir = "TetraOrigin",
  output_stem = "TetraOrigin_input",
  plot_maps = TRUE,
  log = NULL
)

Arguments

maplist

A list of maps. In the first column marker names and in the second their position.

dosage_matrix

An integer matrix with markers in rows and individuals in columns. Either provide the unconverted dosages (i.e. before using the convert_marker_dosages function), or converted dosages (i.e. screened data), in matrix form. The analysis and results are unaffected by this choice, but it may be simpler to understand the results if converted dosages are used. Conversely, it may be advantageous to use the original unconverted dosages if particular marker alleles are being tracked for (e.g.) the development of selectable markers afterwards.

bin_size

Numeric. Size (in cM) of the bins to include. If NULL (by default) then all markers are used (no binning).

bounds

Numeric vector. If NULL (by default) then all positions are included, however if specified then output is limited to a specific region, which is useful for later fine-mapping work.

remove_markers

Optional vector of marker names to remove from the maps. Default is NULL.

outdir

Output directory to which input files for TetraOrigin are written.

output_stem

Character prefix to add to the .csv output filename.

plot_maps

Logical. Plot the marker positions of the selected markers using plot_map.

log

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Examples

## Not run: 
data("integrated.maplist","ALL_dosages")
createTetraOriginInput(maplist=integrated.maplist,dosage_matrix=ALL_dosages,bin_size=10)
## End(Not run)