setSummary: Creation summary statistic files

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

Creation summary statistic files

Description

This function is uses to ouput all the summary files after the creation of the atlas by the following two functions : 'makeAtlasByHotspots' and 'makeAtlasByDistance' is over.

Usage

setSummary(
  atlas,
  list.id,
  probs = TRUE,
  recap.by.segments = FALSE,
  q = 1e-04,
  HBD.threshold = 0.5,
  quality = 95,
  n.consecutive.markers = 5,
  phen.code = c("plink", "R")
)

Arguments

atlas	a atlas object
list.id	you can either : - ignore this parameter if you want to compute HBD, FLOD and HFLOD for individuals who are considerated inbred and with a quality greater or equal to 95 - enter a list of individual for a computation of HBD, FLOD score HFLOD score for them - use "all" for a computation of HBD, FLOD score and HFLOD score for every individual
probs	a flag indicating if the HBD probabilities and FLOD score has been computed for the submaps (default is TRUE)
recap.by.segments	if the summary files has to be computed considering segments or snps (defaut is FALSE) (more information in the documentation of 'makeAtlasByHotspots' or'makeAtlasByDistance' functions)
q	Allows the user to choose the assumed frequency of the mutation involved in the disease for each individual (default is 0.0001)
HBD.threshold	value of the HBD probability threshold used to determine whether a segment is HBD or not (default is 0.5)
quality	The minimum percentage use to assume if a submap is valid (default is 95)
n.consecutive.markers	the number of consecutive markers with a probability equal or greater to the value of the threshold, to be used to find HBDsegments (default is 5)

Details

the function add content to the atlas object.

- summary for likelihood0/likelihood1

- summary for estimation of a and f

- summary for the submaps

- summary for HBD probabilities

- summary for HFLOD

- comutation of HBDsegments

Value

return an atlas containing every summary created

See Also

Fantasio

makeAtlasByDistance

segmentsListByHotspots

festim

setHBDProbAndFLOD

setHBDProbAndFLODBySnps

setHFLOD

submapLikelihood

submapEstim

submapSummary

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