Construct Consensus Genetic Maps and Estimate Recombination Rates


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Documentation for package ‘mapfuser’ version 0.1.2

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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