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

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

Calculate the founder genotype probabilities at each SNP.

Description

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

Usage

  calc.genoprob(data, chr = "all", output.dir = ".", plot = TRUE, 
  array = c("gigamuga", "megamuga", "muga", "other"), 
  sampletype = c("DO", "CC", "DOF1", "other"), method = c("intensity", "allele"), 
  founders, transprobs, snps)

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. When method = allele: geno: Character matrix, num.samples x num.snps, with allele calls (A,C,G,T,H or N) 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.
output.dir	Character string containing the full path where output should be written. The directory must exist already.
plot	Boolean that is true if the user would like to plot a sample chromosome as the model progresses. Default = TRUE.
array	Character string indicating the array type. Must be one of "gigamuga", "megamuga", "muga" or "other". Default equals "gigamuga".
sampletype	Character string containing the type of samples being run. Must be one of "DO", "CC", "DOF1", or "other". Default equals "DO".
method	Character string containing method of genome reconstruction. Must be one of "intensity" or "allele". Default equals "intensity".
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. When method = allele: geno: Character matrix, num.samples x num.snps, with allele calls 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. When sampletype = DOF1 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. This should be "II" for an inbred mutant strain. Sample IDs must be in names. direction: Character string that is either "DOxMUT" if a female DO was crossed with a male mutant mouse or "MUTxDO" if a female mutant mouse was crossed with a male DO. This affects the genotyping of teh X chromosome.
transprobs	Function to call to estimate the transition probabilities between markers for non-DO samples. Not required for DO.
snps	Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively. Not required for DO.

Value

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

Author(s)

Daniel Gatti

Examples

  ## Not run: 
    calc.genoprob(cross, chr.to.run = 1:19, output.dir = "do.data", plot = FALSE, 
	init.means = NULL, init.covars = NULL)
  
## End(Not run)

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