simsnp: Synthetic dataset containing single nucleotide polymorphisms...
In KRIS: Keen and Reliable Interface Subroutines for Bioinformatic Analysis
Description
Usage
Format
Details
References
See Also
Description
The simsnp is the simulated dataset which consists of 3,000 independent SNPs
and 753 individuals belonging to one of three populations (250 individuals
each) and 3 outlying individuals. The pairwise genetic distance between
populations was set to Fst=0.01 as in Balding (1995).
Usage
1
data(example_SNP)
Format
A list with 3 objects
Details
- ind.info
A character matrix of 753 rows and 6 columns representing
individuals and individual information respectively. The columns of
ind.info represents sample_ID, family_ID, father_ID, mother_ID, gender,
and phenotype respectively.
- snp.info
A character matrix of 3,000 rows and 6 columns representing
SNPs and SNP information respectively. The columns of snp.info represents
SNP_CHR (chromosome), SNP_ID, centimorgan, position, allele1, and allele2
respectively.
- snp
A numeric matrix of 753 rows and 3,000 columns representing
individuals and SNPs respectively. The matrix snp contains the number 0, 1,
and 2 representing SNP in additive coding.
References
Balding, D.J., and Nichols, R.A. (1995). A method for quantifying
differentiation between populations at multi-allelic loci and its
implications for investigating identity and paternity. Genetica 96, 3-12.
See Also
KRIS documentation built on Jan. 21, 2021, 5:08 p.m.
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Description Usage Format Details References See Also
Description
The simsnp is the simulated dataset which consists of 3,000 independent SNPs and 753 individuals belonging to one of three populations (250 individuals each) and 3 outlying individuals. The pairwise genetic distance between populations was set to Fst=0.01 as in Balding (1995).
Usage
1 | data(example_SNP)
|
Format
A list with 3 objects
Details
- ind.info
A character matrix of 753 rows and 6 columns representing individuals and individual information respectively. The columns of ind.info represents sample_ID, family_ID, father_ID, mother_ID, gender, and phenotype respectively.
- snp.info
A character matrix of 3,000 rows and 6 columns representing SNPs and SNP information respectively. The columns of snp.info represents SNP_CHR (chromosome), SNP_ID, centimorgan, position, allele1, and allele2 respectively.
- snp
A numeric matrix of 753 rows and 3,000 columns representing individuals and SNPs respectively. The matrix snp contains the number 0, 1, and 2 representing SNP in additive coding.
References
Balding, D.J., and Nichols, R.A. (1995). A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica 96, 3-12.
See Also
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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