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The genotype.saap data is a character matrix with dimensions 120x154. It contains 154 amino acid protein sites across 120 organisms. The data is used in combination with the phenotype.aa data to quantify the association between each amino acid substitution pair and the phenotype vector.
● Data Source:
BioConductor
● Keywords:
● Alias: genotype.saap
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The genotype.saap.msa data is a multiple sequence alignment in Biostrings AAMultipleAlignment format. It contains 120 protein sequences, each with 154 sites (SAAPs). The data is used in combination with the phenotype.aa data to quantify the association between each amino acid substitution pair and the phenotype vector.
● Data Source:
BioConductor
● Keywords:
● Alias: genotype.saap.msa
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The genotype.snp data is a character matrix with dimensions 51x100. It contains 100 SNPs across 51 mouse strains, taken from the publicly available Mouse Hapmap data. We used it in combination with the phenotype.snp data to compute the association between each SNP and the phenotype data.
● Data Source:
BioConductor
● Keywords:
● Alias: genotype.snp
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The genotype.snp.msa data is a multiple sequence alignment in Biostrings DNAMultipleAlignment format. It contains 51 DNA sequences, each with 100 sites (SNPs), taken from the publicly available Mouse Hapmap data. We used it in combination with the phenotype.snp data to compute the association between each SNP and the phenotype data.
● Data Source:
BioConductor
● Keywords:
● Alias: genotype.snp.msa
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runGenphenSaap
(Package: genphen) :
Performing genetic association analysis between SAAPs and phenotypes
This procedure quantifies the association between single amino acid polymorphisms (SAAPs) and phenotypes.
● Data Source:
BioConductor
● Keywords:
● Alias: runGenphenSaap
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runGenphenSnp
(Package: genphen) :
Performing genetic association analysis between SNPs and phenotypes
This procedure computes the association between single nucleotide polymorphisms (SNPs) and phenotypes.
● Data Source:
BioConductor
● Keywords:
● Alias: runGenphenSnp
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The phenotype data is a numerical vector of length 120. It represents 120 measured phenotypes for 120 organisms. We used it as a dependent variable in combination with the genotype.saap data, and quantified the association between each of the SAAP and the phenotype.
● Data Source:
BioConductor
● Keywords: dataset
● Alias: phenotype.saap
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The phenotype data is a numerical vector of length 51. It represents 51 measured phenotypes for 51 laboratory mouse strains. It is to be used as a dependent variable in combination with the SNP genotype data, in order to compute the association between each of the SNPs and the phenotype.
● Data Source:
BioConductor
● Keywords: dataset
● Alias: phenotype.snp
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This procedure plots the results obtained using runGenphenSnp or runGenphenSaap.
● Data Source:
BioConductor
● Keywords:
● Alias: plotGenphenResults
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plotManhattan
(Package: genphen) :
Visualizing genphen results with Manhattan plots
This procedure plots the results obtained using runGenphenSnp or runGenphenSaap.
● Data Source:
BioConductor
● Keywords:
● Alias: plotManhattan
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