Description Usage Arguments Value Author(s) Examples
View source: R/remove_manual.R
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.
1 | remove_manual(MF.obj, to_remove)
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MF.obj |
A mapfuser object genetics maps after map_orient() has been performed |
to_remove |
A list of linkage group ID's to remove |
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
Dennis van Muijen
1 2 3 4 5 6 7 | 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)
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