import_IBD: Import IBD probabilities as estimated by TetraOrigin or...
In polyqtlR: QTL Analysis in Autopolyploid Bi-Parental F1 Populations

import_IBD

R Documentation

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)

polyqtlR documentation built on May 29, 2024, 7:16 a.m.