marker_binning: Perform binning of markers.
In mdavy86/polymapR: Linkage Analysis in Outcrossing Polyploids

Description Usage Arguments Value Examples

marker_binning allows for binning of very closely linked markers and choses one representative.

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marker_binning(dosage_matrix, linkage_df, r_thresh = NA, lod_thresh = NA,
  target_parent = "P1", other_parent = "P2", max_marker_nr = NULL,
  max_iter = 10, log = NULL)

`dosage_matrix`	A dosage `matrix`.
`linkage_df`	A linkage `data.frame`.
`r_thresh`	Numeric. Threshold at which markers are binned. Is calculated if NA.
`lod_thresh`	Numeric. Threshold at which markers are binned. Is calculated if NA.
`target_parent`	A character string specifying the name of the target parent.
`other_parent`	A character string specifying the name of the other parent.
`max_marker_nr`	The maximum number of markers per homologue. If specified, LOD threshold is optimized based on this number.
`max_iter`	Maximum number of iterations to find optimum LOD threshold. Only used if `max_marker_nr` is specified.
`log`	Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

A list with the following components:

`binned_df`	A linkage data.frame with binned markers removed.
`removed`	A data.frame containing binned markers and their representatives.
`left`	Integer. Number markers left.

1 2	data("screened_data3", "all_linkages_list_P1_split") binned_markers<-marker_binning(screened_data3, all_linkages_list_P1_split [["LG2"]][["homologue3"]])