G
(Package: LEA) :
Ancestral allele frequencies from a snmf run
Return the snmf output matrix of ancestral allele frequency matrix for the chosen run with K ancestral populations. For an example, see snmf.
● Data Source:
BioConductor
● Keywords: snmf
● Alias: G
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Q
(Package: LEA) :
Admixture coefficients from a snmf run
Return the snmf output matrix of admixture coefficients for the chosen run with K ancestral populations. For an example, see snmf.
● Data Source:
BioConductor
● Keywords: snmf
● Alias: Q
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LEA is an R package dedicated to landscape genomics and ecological association tests. LEA can run analyses of population structure and genome scans for local adaptation. It includes statistical methods for estimating ancestry coefficients from large genotypic matrices and evaluating the number of ancestral populations (snmf, pca); and identifying genetic polymorphisms that exhibit high correlation with some environmental gradient or with the variables used as proxies for ecological pressures (lfmm). LEA is mainly based on optimized C programs that can scale with the dimension of very large data sets.
● Data Source:
BioConductor
● Keywords: package
● Alias: LEA-package
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adjusted.pvalues
(Package: LEA) :
adjusted p-values from a lfmm run
Return the lfmm output vector of adjusted p-values and the genomic inflation factor using the genomic control method or the lambda inflation factor parameter for the chosen runs with K fatent factors, the d-th variable and the all option. For an example, see lfmm.
● Data Source:
BioConductor
● Keywords: lfmm
● Alias: adjusted.pvalues
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ancestrymap
(Package: LEA) :
code{ancestrymap
Description of the ancestrymap format. The ancestrymap format can be used as an input format for genotypic matrices in the functions pca, lfmm and snmf.
● Data Source:
BioConductor
● Keywords: format
● Alias: ancestrymap, example_ancestrymap
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ancestrymap2geno
(Package: LEA) :
Convert from code{link{ancestrymap
A function that converts from the ancestrymap format to the geno format.
● Data Source:
BioConductor
● Keywords: conversion
● Alias: ancestrymap2geno
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ancestrymap2lfmm
(Package: LEA) :
Convert from code{link{ancestrymap
A function that converts from the ancestrymap format to the lfmm format.
● Data Source:
BioConductor
● Keywords: conversion
● Alias: ancestrymap2lfmm
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cross.entropy
(Package: LEA) :
Cross-entropy criterion from snmf runs
Return the cross-entropy criterion for the chosen runs with K ancestral populations. For an example, see snmf. The cross-entropy criterion is a value based on the prediction of masked genotypes to evaluate the error of ancestry estimation. The criterion will help to choose the best number of ancestral population (K) and the best run among a set of runs in snmf. A smaller value of cross-entropy means a better run in terms of prediction capacity. The cross-entropy criterion can be automatically calculated by the snmf function with the entropy option.
● Data Source:
BioConductor
● Keywords: snmf
● Alias: cross.entropy
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env
(Package: LEA) :
Environmental input file format for code{link{lfmm
Description of the env format. The env format can be used as an input format for the environmental variables in the lfmm function.
● Data Source:
BioConductor
● Keywords: format
● Alias: env
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geno
(Package: LEA) :
Input file for code{link{snmf
Description of the geno format. The geno format can be used as an input format for genotypic matrices in the functions snmf, lfmm, and pca.
● Data Source:
BioConductor
● Keywords: format
● Alias: example_geno, geno
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