remove_manual: Manually remove a linkage group within a specific map and...

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

Description

The quality control passed list of genetic maps may be manually curated further with remove_manual() when the map merging process identified a linkage group witihn a map that gives a high Root Mean Square Error. In the case of interspecific crosses one complete map could be better to exclude all together.

Usage

remove_manual(MF.obj, to_remove)

Arguments

MF.obj	A mapfuser object genetics maps after map_orient() has been performed
to_remove	A list of linkage group ID's to remove

Value

The input object is returned in which the linkage group ID have been removed. Manually removed linkage group ID are saved to the removed_LGIDs config slot

Author(s)

Dennis van Muijen

Examples

fpath <- system.file("extdata", package="mapfuser")
maps <- list.files(fpath, pattern = "-1", full.names = TRUE)
MF.obj <- read_maps(mapfiles = maps, sep = ",", header = TRUE, type = "delim")
MF.obj <- map_qc(MF.obj)
## Remove two linkage groups manually
to_remove <- c("Col-0_Blh-1.csv_1","Col-0_Blh-1.csv_2" )
MF.obj <- remove_manual(MF.obj, to_remove)

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