calc.genoprob {DOQTL} | R Documentation

## 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)

[Package DOQTL version 1.18.0 Index]