IBDConstruct: Construct IBD map
In GOVS-pack/GOVS: Genome optimization via virtual simulation

IBDConstruct

R Documentation

Construct IBD map

Description

A IBD map was constructed of contributions from the parents onto the progeny lines using a hidden Markov model (HMM).

Usage

IBDConstruct(snpParents,snpProgeny,markerInfo,q,
             rou,G,threshold = NULL,omit = T)

Arguments

`snpParents`	A matrix for the parents' genotype, lines in column and marker in row.
`snpProgeny`	An array for the progeny' genotype, marker number must equal to snpParents.
`markerInfo`	A matrix or dataframe with four cols(marker ID, allele, chromsome and physical position) regarding genotypic information.
`q`	The quality of sequencing, range 0 to 1 to define the quality of marker.
`rou`	Correlations between any pairs of flanking markers, that estimated with the offspring-LD level after corrected by parent-LD level, it can be obtained by genetic location.
`G`	Generations that the offsprings decented from the parents.
`threshold`	The threshold of posterior.
`omit`	Whether to omit untraceable segments, default True.

Details

The details see:
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-1930-x#MOESM14
CUBIC: an atlas of genetic architecture promises directed maize improvement
https://github.com/heroalone/HMM-IBD

Value

A list regarding Constructed bin map.

`bin`	Results of IBD analysis (bins matrix), each row represents a bin fragment.
`binsInfo`	Data frame, including bins index, start, end, length of bins locus.

References

Liu H J, Wang X, Xiao Y, et al. CUBIC: an atlas of genetic architecture promises directed maize improvement[J]. Genome biology, 2020, 21(1): 1-17.

https://github.com/heroalone/HMM-IBD

Examples

  ## load example data
  data(IBDTestData)
  ## compute rou from genetic position
  rou = IBDTestData$posGenetic
  rou = diff(rou)
  rou = ifelse(rou<0,0,rou)
  ## constract IBD map of chr10 for one progeny
  IBDRes <- IBDConstruct(snpParents = IBDTestData$snpParents,
  markerInfo = IBDTestData$markerInfo,
  snpProgeny = IBDTestData$snpProgeny,q = 0.97,G = 9,rou = rou)

GOVS-pack/GOVS documentation built on Oct. 9, 2022, 8:29 a.m.