calc.genoprob.intensity: Calculate the founder genotype probabilities at each SNP.

In DOQTL: Genotyping and QTL Mapping in DO Mice

Description

This function performs genome reconstruction using allele intensities. We recommend using allele intensities where available because they often produce better genotype reconstructions.

Usage

  calc.genoprob.intensity(data, chr, founders, snps, output.dir = ".", trans.prob.fxn, 
  plot = FALSE)

Arguments

data	A list with named elements containing the information needed to reconstruct genomes. When method = intensity: x: Numeric matrix, num.samples x num.snps, with X intensities for all samples. Sample IDs and SNP IDs must be in rownames and colnames. y: Numeric matrix, num.samples x num.snps, with Y intensities for all samples. Sample IDs and SNP IDs must be in rownames and colnames. sex: Character vector, containing "M" or "F" indicating sex. Sample IDs must be in names. gen: Character matrix containing the generation of DO outbreeding for each sample. For the DO, this should be "DO" followed by a number with no space between them. For CC mice, this should be CC. Sample IDs must be in names.
chr	Character vector containing chromosomes to run. Must match the chromosome IDs in the snps table. "all" (default) will run all chromosomes.
founders	List containing founder information for non-DO or CC crosses. Not required for DO. When method = intensity: x: Numeric matrix, num.samples x num.snps, with X intensities for all founders and F1s (if available). Sample IDs and SNP IDs must be in rownames and colnames. y: Numeric matrix, num.samples x num.snps, with Y intensities for all founders and F1s (if available). Sample IDs and SNP IDs must be in rownames and colnames. sex: Character vector, containing "M" or "F" indicating sex. Sample IDs must be in names. code: Character vector containing two letter genotype codes for each founder sample. Sample IDs must be in names.
snps	Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively. Not required for DO.
output.dir	Character string containing the full path where output should be written. The directory must exist already.
trans.prob.fxn	FALSEunction to call to estimate the transition probabilities between markers for non-DO samples. Not required for DO.
plot	Boolean that is true if the user would like to plot a sample chromosome as the model progresses. Default = TRUE.

Value

No value is returned. The output files are written to output.dir.

Author(s)

Daniel Gatti

Examples

  ## Not run: 
    calc.genoprob.intensity(data, chr, founders, snps, output.dir = ".", trans.prob.fxn, 
	plot = FALSE)
  
## End(Not run)

DOQTL documentation built on May 6, 2019, 3:09 a.m.