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mapfuser (version 0.1.2)

Construct Consensus Genetic Maps and Estimate Recombination Rates

Description

Construct consensus genetic maps with LPmerge, see Endelman and Plomion (2014) and model the relationship between physical distance and genetic distance using thin-plate regression splines, see Wood (2003) . Perform quality control on input data and visualise intermediate steps.

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Version

Install

install.packages('mapfuser')

Monthly Downloads

1

Version

0.1.2

License

GPL-3

Maintainer

Dennis Muijen

Last Published

October 10th, 2017

Functions in mapfuser (0.1.2)

map_orient

Corrects orientation of input genetic maps
map_qc

Wrapper function of genetic map cleaning per linkage group.
summary.mapfuser

internal position check
map_export

Convert a consensus genetic map created with mapfuser to JoinMap format
map_flip

Invert a linkage group
predict.mapfuser

Predict centiMorgan positions from fitted gam models on the mapfuser object
read_joinmap

Internal function, read genetic maps in JoinMap format
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
read_maps

Read genetic maps
read_ref

Load a reference map
LPmerge_par

Wrapper for multicore and multichromosome merging of maps using the LPmerge
calc_RMSE

Internal function to calculate the Root Mean Square Error to select the maximum interval size.
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
genphys_fit

Model the relationship between genetical and physical genome positions
map_cohesion

Graph check whether maps can be integrated
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