makeAtlasByDistance: Creation of submaps based on distance between markers

In genostats/FEstim: Genetic Data Analyses in Presence of Inbreeding

Creation of submaps based on distance between markers

Description

This function creates n submaps and allows the creation of summary files

Usage

makeAtlasByDistance(
  bedmatrix,
  n = 100,
  segmentsList = segmentsListByDistance(bedmatrix),
  n.cores = 1,
  epsilon = 0.001
)

Arguments

bedmatrix	a bed.matrix object
n	the number of submaps wanted(default is 100)
segmentsList	a list of segment for each chromosomes
n.cores	the number of cores to use if you want to compute submaps using parellelism (default is 1)
epsilon	genotype error rate (default is 0.001)

Details

This function is used to create submaps by randomly picking a marker in each segment in the list of segments given by the argument segmentsList.

After the creation of one submap is finished, the function pass it to 'festim', a function that will computes different values (a, f, p.lrt, likelihood0, likelihood1)

After that we then creates the different summary to interpret easily the results of the computation.

This is done by the function 'setSummary'. This function will call all of the function neccessary to obtained the different summary needed for our data.

You can check all the summary after they are been created by accesing their slots.

When using recap.by.segments with true value, we then consider that the snps picked randomly in a segment is a representant of that segment.

When doing a number N of submaps using the options recap.by.segments,

the different values computed from the

snps picked randomly (a, f, p.lrt, ...) in a segments is considered different values

for the same segments.

Value

return a new list object containing every dataframe and object created

See Also

Fantasio

makeAtlasByHotspots

segmentsListByHotspots

festim

setHBDProb

setFLOD

setHFLOD

recap

setSummary

submapLikelihood

submapEstim

submapSummary

HBDSegments

Examples

 
#Please refer to vignette 

genostats/FEstim documentation built on Feb. 3, 2023, 7:33 p.m.