filter.geno.probs: Remove SNPs where the genotype probabilities are too low for...

In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

Remove SNPs where the genotype probabilities are too low for one founder state

Description

This function accetps the 8 state founder probabilities and searches for SNPs where the founder probabilities are too low for one founder. It removes these SNPs. The QTL mapping model becomes numerically unstable if these SNPs are not removed.

Usage

  filter.geno.probs(geno)

Arguments

geno	Numeric 3D array, with samples in dim[1], states = dim[2] and SNPs in dim[3].

Value

Numeric 3D array, with samples in dim[1], states = dim[2] and SNPs in dim[3]. The SNPs with low probabilities for a single founder have been removed.

Author(s)

Daniel Gatti

See Also

scanone, scanone.perm

Examples

  ## Not run: 
    filter.geno.probs(geno)
  
## End(Not run)

dmgatti/DOQTL documentation built on April 7, 2024, 10:35 p.m.