do.trans.probs: Determine DO transition probabilities
In DOQTL: Genotyping and QTL Mapping in DO Mice
Description
Usage
Arguments
Details
Value
Author(s)
References
Examples
Description
Determine the genotype state transition probability for DO mice of a specific generation between all of the markers on a given chromosome.
Usage
1
do.trans.probs(states, snps, chr = c(1:19, "X"), sex = c("M", "F"), do.gen)
Arguments
states
Character vector of possible genotype states.
snps
Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively.
chr
Character containing the chromosome for which transition probabilities should be calculated.
sex
Character that is one of FALSE or M, indicating the sex to use on the X chromosome.
do.gen
Number vector indicating the DO outbreeding generations to calculate.
Details
This function is used to calculate the transition probabilities between markers for different DO outbreeding generations.
Value
List containing one element per unique DO generation supplied in the do.gen argument. Each list element contains a 3 dimensional array of transition probabilities between each pair of markers (num.states by num.states by num.markers - 1).
Author(s)
Daniel Gatti and Karl Broman
References
Haplotype probabilities in advanced intercross populations.
Broman KW.
G3 (Bethesda). 2012 FALSEeb;2(2):199-202. doi: 10.1534/g3.111.001818. Epub 2012 FALSEeb 1.
PMID: 22384398
Genotype probabilities at intermediate generations in the construction of recombinant inbred lines.
Broman KW.
Genetics. 2012 FALSEeb;190(2):403-12. doi: 10.1534/genetics.111.132647.
PMID: 22345609
Examples
1
## Not run: do.trans.probs(states, snps, chr = c(1:19, "X"), sex = c("M", F), do.gen)
DOQTL documentation built on May 6, 2019, 3:09 a.m.
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Description Usage Arguments Details Value Author(s) References Examples
Description
Determine the genotype state transition probability for DO mice of a specific generation between all of the markers on a given chromosome.
Usage
1 | do.trans.probs(states, snps, chr = c(1:19, "X"), sex = c("M", "F"), do.gen)
|
Arguments
states |
Character vector of possible genotype states. |
snps |
Data.frame containing the marker locations. SNP ID, chromosome, Mb anc cM locations in columns 1 through 4, respectively. |
chr |
Character containing the chromosome for which transition probabilities should be calculated. |
sex |
Character that is one of FALSE or M, indicating the sex to use on the X chromosome. |
do.gen |
Number vector indicating the DO outbreeding generations to calculate. |
Details
This function is used to calculate the transition probabilities between markers for different DO outbreeding generations.
Value
List containing one element per unique DO generation supplied in the do.gen argument. Each list element contains a 3 dimensional array of transition probabilities between each pair of markers (num.states by num.states by num.markers - 1).
Author(s)
Daniel Gatti and Karl Broman
References
Haplotype probabilities in advanced intercross populations. Broman KW. G3 (Bethesda). 2012 FALSEeb;2(2):199-202. doi: 10.1534/g3.111.001818. Epub 2012 FALSEeb 1. PMID: 22384398 Genotype probabilities at intermediate generations in the construction of recombinant inbred lines. Broman KW. Genetics. 2012 FALSEeb;190(2):403-12. doi: 10.1534/genetics.111.132647. PMID: 22345609
Examples
1 | ## Not run: do.trans.probs(states, snps, chr = c(1:19, "X"), sex = c("M", F), do.gen)
|
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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