GenABEL (version 1.8-0)

genome-wide SNP association analysis

Description

a package for genome-wide association analysis between quantitative or binary traits and single-nucleotide polymorphisms (SNPs).

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Version

Install

install.packages('GenABEL')

Monthly Downloads

357

Version

1.8-0

License

GPL (>= 2)

Homepage

http://www.genabel.org

Maintainer

Yurii Aulchenko

Last Published

December 27th, 2013

Functions in GenABEL (1.8-0)

as.character.gwaa.data

Attempts to convert genotypic part of gwaa.data to character

as.data.frame.gwaa.data

Attempts to convert snp.data to "hsgeno"

as.double.gwaa.data

Attempts to convert gwaa.data to double

as.character.snp.strand

Attempts to convert internal strand-class to character

add.phdata

Adds phenotypic variables to gwaa.data object

as.double.snp.data

Attempts to convert snp.data to double

as.character.snp.coding

Attempts to convert internal snp.coding-class to character

arrange_probabel_phe

arranges ProbABEL phenotype-file

as.character.snp.data

Attempts to convert snp.data to character

add.plot

function to plot additional GWAA results

catable

function to generate summary table for quantitative data

as.genotype.snp.data

Attempts to convert snp.data to "genotype"

as.genotype

Attempts to convert object to "genotype"

as.genotype.gwaa.data

Attempts to convert gwaa.data to "genotype"

as.hsgeno.gwaa.data

Attempts to convert gwaa.data to "hsgeno"

as.hsgeno.snp.data

Attempts to convert snp.data to "hsgeno"

autosomal

Function telling all autosomal SNPs

blurGenotype

blur genotype calls into probabilites

ccfast

fast case-control analysis

as.hsgeno

Attempts to convert object to "hsgeno"

convert.snp.tped

function to convert genotypic data in transposed-ped format (.tped and .tfam) to internal genotypic data formatted file

convert.snp.ped

function to convert genotypic data in pedigree fromat (+map) to internal data format

convert.snp.text

function to convert integer genotypic data file to raw internal data formated file

convert.snp.affymetrix

function to convert genotypic data from Affymetrix to internal format

cocohet

Test for compound heterozygote effects

checkPackageVersionOnCRAN

checks what is the version of package on CRAN

convert.snp.illumina

function to convert genotypic data from Illumina/Affymetrix to internal format

check.marker

function to do genotypic quality control

check.marker-class

Class "check.marker"

convert.snp.mach

function to convert genotypic data from MACH format to internal data format

egscore

Fast score test for association, corrected with PC

descriptives.trait

Function to generate descriptive summary tables for phenotypic data

emp.ccfast

Genome-wide significance for a case-control GWA scan

dprfast

Estimates D' between multiple markers

descriptives.marker

Function to generate descriptive summary tables for genotypic data

del.phdata

delete phenotypes from phdata

crnames

Return column and row names

egscore.old

Fast score test for association, corrected with PC

descriptives.scan

Function to describe "top" hits in GWA scan

emp.qtscore

Genome-wide significance for a GWA scan

export.merlin

function to export GenABEL data in merlin format

export.impute

function to export GenABEL data in IMPUTE format

extract.annotation.impute

extracts SNP annotation from IMPUTE files

export.plink

Export GenABEL data in PLINK format

estlambda

Estimate the inflation factor for a distribution of P-values

formetascore

function to run GWA analysis oriented for future meta-analysis

GASurv

Makes survival data object for reg.gwaa

findRelatives

guesses relations between individuals

extract.annotation.mach

extracts SNP annotation from MACH/HapMap legend files

GenABEL

GWAS in R

grammar

GRAMMAR test for association in samples with genetic structure

makeTransitionMatrix

Genotype transition probabilities matrices

gwaa.data-class

Class "gwaa.data"

mach2databel

converts MACH-imputed files to DatABEL (filevector) format

impute2databel

converts IMPUTE-imputed files to DatABEL (filevector) format

HWE.show

show HWE tables

getLogLikelihoodGivenRelation

computes logLik of two blurGenotypes

generateOffspring

simulates offspring's genotypes

impute2mach

converts IMPUTE to MACH files

load.gwaa.data

function to load GWAA data

qvaluebh95

Computes Benjamini-Hochberg (95) q-value

qtscore

Fast score test for association

perid.summary

Summary of marker data per person

PGC

Polynomial genomic control

plot.scan.gwaa

function to plot GWAA results

plot.scan.gwaa.2D

function to plot 2D scan results

plot.check.marker

plots "check.marker" object

scan.gwaa.2D-class

Class "scan.gwaa.2D"

polygenic_hglm

Estimation of polygenic model

scan.haplo.2D

runs haplo.score.slide with all pairs of markers in a region

snp.data

creates an snp.data object

VIFGC

Genomic control for various model of inheritance using VIF

VIFGC_ovdom

Genomic control for over-dominant model of inheritance using VIF

snp.mx-class

Class "snp.mx"

snp.subset

function to subset objects of class scan.gwaa and check.marker

snps.cell-class

Class "snps.cell"

summary.scan.gwaa

Shortcut to 'descriptives...

summary.snp.data

function to summary GWAA data

scan.glm.2D

Scans regional data allowing for gene-gene interaction using glm

save.gwaa.data

function to save gwaa.data object

patch_strand

function to change strand

npsubtreated

non-parametric trait "imputations" in treated people

reconstructNPs

reconstruct nuclear families

recodeChromosome

Change chromosomal coding

rhofast

Estimates rho between multiple markers

rntransform

Rank-transformation to normality

sortmap.internal

Internal function for map-sorting

sset

Internal use function for class snp.mx-class

Xfix

function to set impossible genotypes as missing

merge.gwaa.data

function to merge objects of gwaa.data-class

refresh.gwaa.data

Updates an object from old to new GenABEL format

redundant

function to do redundancy check

merge.snp.data

function to merge objects of snp.data-class

scan.gwaa-class

Class "scan.gwaa"

scan.glm

Scan GWA data using glm

snp.coding-class

Class "snp.coding"

mlreg.p

EXPERIMENTAL Linear and logistic regression and Cox models for genome-wide SNP data

mlreg

Linear and logistic regression and Cox models for genome-wide SNP data

snp.data-class

Class "snp.data"

r2fast

Estimates r2 between multiple markers

scan.haplo

r2fast.old

Estimates r2 between multiple markers

snp.names

extracts names of SNPs in a region

show.ncbi

Shows the region on NCBI map

snp.strand-class

Class "snp.strand"

summary.gwaa.data

function to summarise GWAA data

summary.check.marker

Summary of check.marker object

ztransform

Transformation to standard Normal