Fantasio: Wrapper for the package Fantasio

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

Wrapper for the package Fantasio

Description

This function is used as a wrapper for the package Fantasio to create segments list and submaps

Usage

Fantasio(
  bedmatrix,
  segments = c("Hotspots", "Distance"),
  segment.options,
  n = 100,
  n.cores = 1,
  epsilon = 0.001,
  run.proba = TRUE,
  recap.by.segments = FALSE,
  verbose = TRUE,
  run.logistic = FALSE,
  HBD.threshold = 0.5,
  q = 1e-04,
  quality = 95,
  n.consecutive.markers = 5,
  phen.code = c("plink", "R"),
  expl.var = c("FLOD", "HBD_prob"),
  cov.df,
  cov
)

Arguments

bedmatrix	a bed.matrix
segments	The method to use for submap creation ("Hotspots" or "Distance")
segment.options	a list of arguments to the function that will create the segments list
n	the number of submaps (default is 100)
n.cores	number of cores to use if you want to compute submaps using parellelism (default is 1)
epsilon	genotype error rate (default is 0.001)
run.proba	whether you want to computes HBD, FLOD score and HFLOD score (default is TRUE)
recap.by.segments	if you want the summary of probabilities by snps or by segments (default is FALSE)
verbose	whether you want informations about computations (default is TRUE)
run.logistic	whether you want to run the logistic regression (default is FALSE)
HBD.threshold	value of the HBD probability threshold used to determine whether a segment is HBD or not (default is 0.5)
q	assumed frequency of the mutation involved in the disease for each individual (default is 0.0001)
quality	minimal quality (in %) to include an inbred individual into the analysis (default is 95)
n.consecutive.markers	number of consecutive markers with a probability equal or greater to the value of 'HBD.threshold', used to find HBDsegments
phen.code	phenotype coding : - 'R' : 0:control ; 1:case ; NA:unknown - 'plink' : 1:control ; 2:case ; 0/-9/NA:unknown (default)
cov.df	a dataframe containing covariates for logistic regression
cov	covariates of interest for logistic regression such as 'age', 'sex' , ... if missing, all covariates of the dataframe are considered

Details

This function is a wrapper to make the usage of the package easier. The function calls different functions:

The first function, 'segmentsListByDistance' or 'segmentsListByHotspots', is used to create a list of segments.

The second function, 'makeAtlasByDistance' or 'makeAtlasByHotspots', is used to create submaps.

Depending on the value of the 'segments' argument (Hotspots or Distance), the segments are created based on recombination hotspots, or based on markers' distance. In the latter case, the submaps are made by picking a random marker in every segments and going through each segment from left to right using a given step (by default it is 0.5 cM).

The arguments that can be included in 'segment.options' are described in 'segmentsListByDistance' and 'segmentsListByHotspots'.

If 'recap.by.segments = FALSE', the quantities such as HBD probabilities, FLOD, HFLOD, are recapitulated SNP by SNP, by taking the mean value accross submaps in which the SNP appear. If 'recap.by.segments = TRUE' (only with 'segments = "Hotspots"'), these quantities are averaged over all SNPs sampled in a segment.

See Also

read.bed.matrix

segmentsListByDistance

makeAtlasByDistance

makeAtlasByHotspots

makeAtlasByHotspots

Examples

#Please refer to vignette 

genostats/Fantasio documentation built on Feb. 2, 2023, 5:28 p.m.