R Graphical Manual

Last data update: 2014.03.03

Data Source

R Release (3.2.3)
CranContrib
BioConductor
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Classification

Results 1 - 10 of 23 found.
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bed.matrix-class (Package: gaston) : Class code{"bed.matrix"

S4 class for SNP genotype matrices

● Data Source: CranContrib
● Keywords: classes
● Alias: [,bed.matrix,logical,logical,missing-method, [,bed.matrix,logical,missing,missing-method, [,bed.matrix,logical,numeric,missing-method, [,bed.matrix,missing,logical,missing-method, [,bed.matrix,missing,numeric,missing-method, [,bed.matrix,numeric,logical,missing-method, [,bed.matrix,numeric,missing,missing-method, [,bed.matrix,numeric,numeric,missing-method, %*%,bed.matrix,matrix-method, %*%,bed.matrix,vector-method, %*%,matrix,bed.matrix-method, %*%,vector,bed.matrix-method, as.matrix,bed.matrix-method, bed.matrix, bed.matrix-class, cbind, cbind,bed.matrix-method, coerce,bed.matrix,matrix-method, coerce,bed.matrix,vector-method, coerce,matrix,bed.matrix-method, coerce,vector,bed.matrix-method, dim,bed.matrix-method, head,bed.matrix-method, matrix,data.frameOrNULL,data.frameOrNULL-method, mu, mu,bed.matrix-method, mu<-, mu<-,bed.matrix-method, p, p,bed.matrix-method, p<-, p<-,bed.matrix-method, rbind, rbind,bed.matrix-method, show,bed.matrix-method, sigma, sigma,bed.matrix-method, sigma<-, sigma<-,bed.matrix-method, standardize, standardize,bed.matrix-method, standardize<-, standardize<-,bed.matrix-method
● 0 images

read.vcf (Package: gaston) : Create a code{link{bed.matrix

Create a bed.matrix from a .vcf file.

● Data Source: CranContrib
● Keywords: vcf files
● Alias: read.vcf
● 0 images

set.genomic.sex (Package: gaston) : Genomic Sex

Returns an updated bed.matrix with a new variable for the genomic sex of each individual.

● Data Source: CranContrib
● Keywords: Genomic Sex
● Alias: set.genomic.sex
● 0 images

select.inds (Package: gaston) : Subsetting from a code{link{bed.matrix

Return subset of individuals satisfying a condition.

● Data Source: CranContrib
● Keywords:
● Alias: select.inds
● 0 images

bed.loadings (Package: gaston) : SNP loadings

Compute the loadings corresponding to given PCs.

● Data Source: CranContrib
● Keywords: loadings
● Alias: bed.loadings
● 0 images

reshape.GRM (Package: gaston) : Reshape a Genetic Relationship Matrix

Reshapes a GRM into a data frame listing relationship of (possibly all) pairs of individuals. Options are provided to specify ranges of relationship values to include or exclude. This is useful in the Quality Control process.

● Data Source: CranContrib
● Keywords: Genetic Relationship Matrix
● Alias: reshape.GRM
● 0 images

gaston-package (Package: gaston) : gaston

Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalisation trick).

● Data Source: CranContrib
● Keywords: Genetics, SNP, association study, linear mixed models
● Alias: gaston, gaston-package
● 0 images

lik.contour (Package: gaston) : Contour plot for two parameters likelihood

Create a contour plot (superimposed with a heat map)

● Data Source: CranContrib
● Keywords: Heat map
● Alias: lik.contour
● 0 images

set.stats (Package: gaston) : Basic statistics for a code{link{bed.matrix

Return an updated bed.matrix with new variables for several basic statistics.

● Data Source: CranContrib
● Keywords: Genetic, Statistics
● Alias: set.stats
● 0 images

lmm.diago.likelihood (Package: gaston) : Likelihood of a linear mixed model

Compute the Restricted Likelihood of a linear mixed model, using the "diagonalization trick".

● Data Source: CranContrib
● Keywords: Eigen decomposition, Likelihood
● Alias: lmm.diago.likelihood
● 0 images