faster_IBD: Extremely fast estimation of identity-by-descent (IBD)...

In Alethere/SmoothDescent: Application of map-based genotype correction algorithm Smooth Descent

Extremely fast estimation of identity-by-descent (IBD) probabilities.

Description

The method of "quick-and-dirty" IBD estimation was originally developed by Bourke (2014) for tetraploid data only, and was subsequently generalised by van Geest et al. (2017). Can be useful for a first quick analysis, particularly in large hexaploid datasets. However, the higher accuracy of IBD probabilities generated by hmm_IBD makes that function the preferred choice.

Usage

faster_IBD(
  phased_maplist,
  dosage_matrix,
  map_function = "haldane",
  ploidy,
  ploidy2 = NULL,
  fix_threshold = 0.1,
  factor_dist = 1,
  ncores = 1,
  p1name = "P1",
  p2name = "P2",
  method.exp = "simple",
  double_reduction = T
)

Arguments

phased_maplist	A list of linkage maps calculated by polymapR::create_phased_maplist
dosage_matrix	An integer matrix with markers in rows and individuals in columns
map_function	The mapping function to calculate recombination frequency based on map distance (haldane or kosambi)
ploidy	Ploidy level of parents or of the first parent
ploidy2	Ploidy level of the second parent. By default NULL, if parents have equal ploidy levels.
fix_threshold	The threshold to fix the IBD probabilities while correcting for the sum of probabilities.
factor_dist	Factor to increase or decrease the recombination frequencies as calculated from the map distances.
ncores	Number of cores to use for multi-core processing.
p1name	Name of parent 1 in the column names of dosage_matrix
p2name	Name of parent 2 in the column names of dosage_matrix
method.exp	Model to use for probability expansion. Either "simple" or "interval"

Value

A nested list (with the same length as phased_maplist). Each list element contains the following items:

IBDtype	Always "haplotypeIBD" for the output of this function
IBDarray	An array of IBD probabilities. The dimensions of the array are: markers, homologues and individuals.
map	Integrated linkage map positions of markers used in IBD calculation
parental_phase	The parental marker phasing, coded in 1 and 0's
biv_dec	NULL
gap	The gap size used in IBD interpolation, by default NULL. See spline_IBD
genocodes	NULL
pairing	NULL
ploidy	ploidy of parent 1
ploidy2	ploidy of parent 2
method	The method used, here "heur" (heuristic)
error	The error prior used, not relevant here thus NULL

References

Bourke P.M. (2014) QTL analysis in polyploids: Model testing and power calculations. Wageningen University (MSc thesis)

Examples

data("phased_maplist.4x","SNP_dosages.4x")
IBD_list.4x <- fast_IBD(phased_maplist = phased_maplist.4x,
                        dosage_matrix = SNP_dosages.4x,
                        ploidy = 4)

Alethere/SmoothDescent documentation built on Oct. 21, 2023, 7:11 a.m.