# Construct Consensus Genetic Maps and Estimate Recombination Rates

## Documentation for package ‘mapfuser’ version 0.1.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

calc_RMSE | Internal function to calculate the Root Mean Square Error to select the maximum interval size.
check_anchors | Replace sub-linkage groups (e.g. 1.1, 1.2) with truncated linkage group number and split per chromosome for easy integration
check_cM | internal position check
genphys_fit | Model the relationship between genetical and physical genome positions
LPmerge_par | Wrapper for multicore and multichromosome merging of maps using the LPmerge
map_cohesion | Graph check whether maps can be integrated
map_export | Convert a consensus genetic map created with mapfuser to JoinMap format
map_flip | Invert a linkage group
map_orient | Corrects orientation of input genetic maps
map_qc | Wrapper function of genetic map cleaning per linkage group.
map_split | Replace sub-linkage groups (e.g. 1.1, 1.2) with truncated linkage group number and split per chromosome for easy integration
plot.mapfuser | Visualise mapfuser object data
predict.mapfuser | Predict centiMorgan positions from fitted gam models on the mapfuser object
read_joinmap | Internal function, read genetic maps in JoinMap format
read_maps | Read genetic maps
read_ref | Load a reference map
remove_manual | Manually remove a linkage group within a specific map and update man networks and minimum spanning tree
select_result | Select result from mapfuser
summary.mapfuser | internal position check