saveMarkerModels: DEPRECATED: Function to fit mixture models for series of...

In fitPoly: Genotype Calling for Bi-Allelic Marker Assays

DEPRECATED: Function to fit mixture models for series of markers and save the results to files

Description

This is the old name of the function 'fitMarkers()', the main function of 'fitPoly'. It is kept only for backwards-compatibility. The only difference between the two is the default parameter of the genotyping probability threshold 'p.threshold', it is 0.99 in 'saveMarkerModels()' (as was originally set) and it is 0.9 in the current 'fitMarkers()'.

Usage

saveMarkerModels(..., p.threshold = 0.99)

Arguments

...	All parameters allowed in the function 'fitMarkers()'. For a full description see the help of that function.
p.threshold	The minimum P-value required to assign a genotype (dosage) to a sample; default 0.99 (very stringent). If the P-value for all possible genotypes is less than p.threshold the sample is assigned genotype NA. Set to 1 to disable this filter.

Value

See 'fitMarkers()' documentation for a full description.

fitPoly documentation built on April 3, 2025, 8:58 p.m.