polyqtlR (version 0.1.1)

import_IBD: 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
)

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

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.

Examples

if (FALSE) {
## 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")
}