R Graphical Manual

Last data update: 2014.03.03

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R Release (3.2.3)
CranContrib
BioConductor
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Results 1 - 10 of 27 found.
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LD (Package: SNPassoc) : max-statistic for a 2x3 table

Compute pairwise linkage disequilibrium between genetic markers

● Data Source: CranContrib
● Keywords: utilities
● Alias: LD, LD.setupSNP, LD.snp, LDplot, LDtable
● 0 images

tableHWE (Package: SNPassoc) : Test for Hardy-Weinberg Equilibrium

Test the null hypothesis that Hardy-Weinberg equilibrium holds in cases, controls and both populations.

● Data Source: CranContrib
● Keywords: utilities
● Alias: print.tableHWE, tableHWE
● 0 images

is.Monomorphic (Package: SNPassoc) : Check whether a SNP is Monomorphic

This function verifies when a SNP is Monomorphic

● Data Source: CranContrib
● Keywords: internal
● Alias: is.Monomorphic
● 0 images

plotMissing (Package: SNPassoc) : Plot of missing genotypes

Plot a grid showing which genotypes are missing

● Data Source: CranContrib
● Keywords: utilities
● Alias: plotMissing
● 2 images

inheritance (Package: SNPassoc) : Collapsing (or recoding) genotypes into different categories (generally two) depending on a given genetic mode of inheritance

codominant function recodifies a variable having genotypes depending on the allelic frequency in descending order.

● Data Source: CranContrib
● Keywords: utilities
● Alias: additive, codominant, dominant, geneticModel, inheritance, overdominant, recessive
● 0 images

association (Package: SNPassoc) : Association analysis between a single SNP and a given phenotype

This function carries out an association analysis between a single SNP and a dependent variable (phenotype) under five different genetic models (inheritance patterns): codominant, dominant, recessive, overdominant and log-additive. The phenotype may be quantitative or categorical. In the second case (e.g. case-control studies) this variable must be of class 'factor' with two levels.

● Data Source: CranContrib
● Keywords: utilities
● Alias: association, print.snpOut
● 0 images

permTest (Package: SNPassoc) : Permutation test analysis

This function extract the p values for permutation approach performed using scanWGassociation function

● Data Source: CranContrib
● Keywords: utilities
● Alias: permTest, plot.permTest, print.permTest
● 0 images

WGassociation (Package: SNPassoc) : Whole genome association analysis

This function carries out a whole genome association analysis between the SNPs and a dependent variable (phenotype) under five different genetic models (inheritance patterns): codominant, dominant, recessive, overdominant and log-additive. The phenotype may be quantitative or categorical. In the second case (e.g. case-control studies) this variable must be of class 'factor' with two levels.

● Data Source: CranContrib
● Keywords: utilities
● Alias: WGassociation, WGstats, [.WGassociation, additive.WGassociation, codominant.WGassociation, dominant.WGassociation, labels.WGassociation, overdominant.WGassociation, print.WGassociation, pvalues, pvalues.WGassociation, recessive.WGassociation, summary.WGassociation
● 2 images

int (Package: SNPassoc) :

This is a special function used for 'haplo.interaction' function. It identifies the variable that will interact with the haplotype estimates. Using int() in a formula implies that the interaction term between this variable and haplotypes is included in 'haplo.glm' function.

● Data Source: CranContrib
● Keywords: utilities
● Alias: int
● 0 images

maxstat (Package: SNPassoc) : max-statistic for a 2x3 table

Computes the asymptotic p-value for max-statistic for a 2x3 table

● Data Source: CranContrib
● Keywords: utilities
● Alias: maxstat, maxstat.default, maxstat.matrix, maxstat.setupSNP, maxstat.table, print.maxstat
● 0 images