import_IBD {polyqtlR}

Import IBD probabilities as estimated by TetraOrigin or PolyOrigin

Description

Imports the IBD probability output of TetraOrigin (Mathematica software) or PolyOrigin (julia software) into the same format as natively-estimated IBD probabilities from the polyqtlR package.

Usage

import_IBD(
  method,
  folder = NULL,
  filename,
  bivalent_decoding = TRUE,
  error = 0.01,
  log = NULL
)

Arguments

method

The method used for IBD estimation, either "TO" for TetraOrigin or "PO" for PolyOrigin

folder

The path to the folder in which the Tetra/PolyOrigin (ie. TetraOrigin or PolyOrigin) output is contained, default is NULL if files are in working directory.

filename

If method = "TO", the (vector of) character filename stem(s) of the .csv file(s) containing the output of TetraOrigin (stem = without ".csv"). Should be in order according to LG/chromosome numbering. If method = "PO", then simply specify the PolyOrigin filename stem here (as the output is not split into separate linkage groups in PolyOrigin). A PolyOrigin file with name <filename>_polyancestry.csv and its corresponding log file <filename>.log will then be searched for.

bivalent_decoding

Logical, if method = "TO" you must specify TRUE if only bivalent pairing was allowed in TetraOrigin (in offspring deciding step), otherwise specify FALSE if multivalent pairing was also allowed. If method = "PO", this will be automatically detected, so no need to specify (will be ignored).

error

If method = "TO", the offspring error prior used in the offspring decoding step of TetraOrigin, by default assumed to be 0.01. For method = "PO", this is automatically read in.

log

Character string specifying the log filename to which standard output should be written. If NULL log is send to stdout.

Value

Returns a list with the following items:

IBDtype :

Always "genotypeIBD" for the output of TetraOrigin

IBDarray :

An array of IBD probabilities. The dimensions of the array are: markers, genotype classes and individuals.

map :

Integrated linkage map positions of markers used in IBD calculation

parental_phase :

The parental marker phasing as used by TetraOrigin, recoded in 1 and 0's

marginal.likelihoods :

A list of marginal likelihoods of different valencies, currently NULL

valency :

The predicted valency that maximised the marginal likelihood, per offspring. Currently NULL

offspring :

Offspring names

biv_dec :

Logical, the bivalent_decoding parameter specified.

gap :

The gap size used in IBD interpolation if performed by spline_IBD. At this stage, NULL

genocodes :

Ordered list of genotype codes used to represent different genotype classes.

pairing :

log likelihoods of each of the different pairing scenarios considered (can be used e.g. for post-mapping check of preferential pairing)

ploidy :

The ploidy of parent 1, by default assumed to be 4

ploidy2 :

The ploidy of parent 2, by default assumed to be 4

method :

The method used, either "hmm_TO" (TetraOrigin) or "hmm_PO" (PolyOrigin)

error :

The error prior used in the calculation in TetraOrigin, assumed to be 0.01

Examples

## Not run: 
## These examples demonstrate the function call for both methods, but won't run without input files
## from either package, hence this call will normally result in an Error:
IBD_TO <- import_IBD(method = "TO", filename = paste0("test_LinkageGroup",1:5,"_Summary"),
bivalent_decoding = FALSE, error = 0.05)
## Equivalent call for PolyOrigin output:
IBD_PO <- import_IBD(method = "PO",filename = "test")

## End(Not run)