pvalqq.plotting plots a Q-Q plot of the p-values computed.
● Data Source:
CranContrib
● Keywords: internal
● Alias: pvalqq.plotting
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compute.pval
(Package: pcadapt) :
Principal Components p-values
compute.pval computes p-values for each genetic marker, depending on the test statistics distribution.
● Data Source:
CranContrib
● Keywords: internal
● Alias: compute.pval
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manhattanPlot displays a Manhattan plot which represents the p-values for each SNP for a particular test statistic.
● Data Source:
CranContrib
● Keywords: internal
● Alias: manhattan.plotting
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score.plotting
(Package: pcadapt) :
Principal Components Analysis Scores Plot
"score.plotting" plots the projection of the individuals onto the first two principal components.
● Data Source:
CranContrib
● Keywords: internal
● Alias: score.plotting
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get.pc
(Package: pcadapt) :
Get the principal component the most associated with a genetic marker
get.pc returns a data frame such that each row contains the index of the genetic marker and the principal component the most correlated with it.
● Data Source:
CranContrib
● Keywords: internal
● Alias: get.pc
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read.pcadapt converts .vcf and .ped files to an appropriate type of file readable by pcadapt. You may find the converted file in the current directory.
● Data Source:
CranContrib
● Keywords:
● Alias: read.pcadapt
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This package has been developed to provide statistical tools for outlier detection based on Principal Component Analysis.
● Data Source:
CranContrib
● Keywords: package
● Alias: pcadapt-package
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get.score.color allows the user to display individuals of the same pre-defined population with the same color when using the option "scores" in pcadapt.
● Data Source:
CranContrib
● Keywords: internal
● Alias: get.score.color
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corpca
(Package: pcadapt) :
Principal Component Analysis based on the correlation matrix
corpca is an auxiliary function that performs principal components analysis on a dataset. It returns an object x which contains the loadings, the scores and the singular values of the K first principal components. It handles missing values in a dataset and actually computes the eigen elements of the n x n covariance matrix, where n is the number of individuals.
● Data Source:
CranContrib
● Keywords: internal
● Alias: corpca
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get.pop.names retrieves the population names from the population file.
● Data Source:
CranContrib
● Keywords: internal
● Alias: get.pop.names
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providing 
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