genome-wide SNP association analysis


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Documentation for package ‘GenABEL’ version 1.4-2

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A C D E F G H I L M N P Q R S X Z misc

-- --

GenABEL-package GenABEL: an R package for Genome Wide Association Analysis

-- A --

add.phdata Adds phenotypic variables to gwaa.data object
add.plot function to plot additional GWAA results
as.character.gwaa.data Attempts to convert genotypic part of gwaa.data to character
as.character.snp.coding Attempts to convert internal snp.coding-class to character
as.character.snp.data Attempts to convert snp.data to character
as.character.snp.strand Attempts to convert internal strand-class 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.double.snp.data Attempts to convert snp.data to double
as.genotype Attempts to convert object to "genotype"
as.genotype.gwaa.data Attempts to convert gwaa.data to "genotype"
as.genotype.snp.data Attempts to convert snp.data to "genotype"
as.hsgeno Attempts to convert object to "hsgeno"
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

-- C --

catable function to generate summary table for quantitative data
ccfast fast case-control analysis
check.marker function to do genotypic quality control
check.marker-class Class "check.marker"
check.trait function to do primitive trait quality control
coerce,snp.coding,character-method Class "snp.coding"
coerce,snp.data,character-method Class "snp.data"
coerce,snp.data,genotype-method Class "snp.data"
coerce,snp.data,hsgeno-method Class "snp.data"
coerce,snp.data,numeric-method Class "snp.data"
coerce,snp.mx,character-method Class "snp.mx"
coerce,snp.mx,numeric-method Class "snp.mx"
coerce,snp.strand,character-method Class "snp.strand"
convert.snp.affymetrix function to convert genotypic data from Affymetrix to internal format
convert.snp.illumina function to convert genotypic data from Illumina/Affymetrix to internal format
convert.snp.mach function to convert genotypic data from MACH format to internal data format
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.tped function to convert genotypic data in transposed-ped format (.tped and .tfam) to internal genotypic data formatted file
crnames Return column and row names

-- D --

descriptives.marker Function to generate descriptive summary tables for genotypic data
descriptives.scan Function to describe "top" hits in GWA scan
descriptives.trait Function to generate descriptive summary tables for phenotypic data
dprfast Estimates D' between multiple markers

-- E --

egscore Fast score test for association, corrected with PC
egscore.old Fast score test for association, corrected with PC
emp.ccfast Genome-wide significance for a case-control GWA scan
emp.qtscore Genome-wide significance for a GWA scan
estlambda Estimate the inflation factor for a distribution of P-values
export.merlin function to export GenABEL data in merlin format

-- F --

formetascore function to run GWA analysis oriented for future meta-analysis

-- G --

GASurv Makes survival data object for reg.gwaa
ge03d2 GWA-type data on few small region
ge03d2c GWA-type data on few small region
ge03d2ex GWA-type data on few small region
GenABEL GenABEL: an R package for Genome Wide Association Analysis
grammar Approximate score test for association in related people
gwaa.data-class Class "gwaa.data"

-- H --

hom function to compute average homozygosity within a person
hom.old function to compute average homozygosity within a person
HWE.show show HWE tables

-- I --

ibs Computes (average) Idenity-by-State for a set of people and markers
ibs.old Computes (average) Idenity-by-State for a set of people and markers

-- L --

load.gwaa.data function to load GWAA data

-- M --

merge.gwaa.data function to merge objects of gwaa.data-class
merge.snp.data function to merge objects of snp.data-class
mlreg Linear and logistic regression and Cox models for genome-wide SNP data
mlreg.p EXPERIMENTAL Linear and logistic regression and Cox models for genome-wide SNP data
mmscore Score test for association in related people

-- N --

npsubtreated non-parametric trait "imputations" in treated people

-- P --

perid.summary Summary of marker data per person
plot, check.marker-method Class "check.marker"
plot, scan.gwaa-method Class "scan.gwaa"
plot, scan.gwaa.2D-method Class "scan.gwaa.2D"
plot.check.marker plots "check.marker" object
plot.scan.gwaa function to plot GWAA results
plot.scan.gwaa.2D function to plot 2D scan results
polygenic Estimation of polygenic model
pop2.ids GWA-type data on few small region

-- Q --

qc.nostr GWA-type data on few small region
qc.str GWA-type data on few small region
qtscore Fast score test for association
qvaluebh95 Computes Benjamini-Hochberg (95) q-value

-- R --

r2fast Estimates r2 between multiple markers
r2fast.old Estimates r2 between multiple markers
redundant function to do redundancy check
refresh.gwaa.data Updates an object from old to new GenABEL format
reg.gwaa Linear and logistic regression and Cox models for genome-wide SNP data
rhofast Estimates rho between multiple markers
rntransform Rank-transformation to normality

-- S --

save.gwaa.data function to save gwaa.data object
scan.glm Scan GWA data using glm
scan.glm.2D Scans regional data allowing for gene-gene interaction using glm
scan.gwaa-class Class "scan.gwaa"
scan.gwaa.2D-class Class "scan.gwaa.2D"
scan.haplo scan.haplo
scan.haplo.2D runs haplo.score.slide with all pairs of markers in a region
show,gwaa.data-method Class "gwaa.data"
show,snp.coding-method Class "snp.coding"
show,snp.data-method Class "snp.data"
show,snp.mx-method Class "snp.mx"
show,snp.strand-method Class "snp.strand"
show.ncbi Shows the region on NCBI map
snp.coding-class Class "snp.coding"
snp.data creates an snp.data object
snp.data-class Class "snp.data"
snp.mx-class Class "snp.mx"
snp.names extracts names of SNPs in a region
snp.strand-class Class "snp.strand"
snp.subset function to subset objects of class scan.gwaa and check.marker
snps.cell-class Class "snps.cell"
srdta GWA-type data on small region
sset Internal use function for class snp.mx-class
summary, check.marker-method Class "check.marker"
summary,gwaa.data-method Class "gwaa.data"
summary,snp.data-method Class "snp.data"
summary,snp.mx-method Class "snp.mx"
summary.check.marker Summary of check.marker object
summary.gwaa.data function to summarise GWAA data
summary.snp.data function to summary GWAA data

-- X --

Xfix function to set impossible genotypes as missing

-- Z --

ztransform Transformation to standard Normal

-- misc --

[,gwaa.data,ANY,ANY,ANY-method Class "gwaa.data"
[,snp.coding,ANY,missing,missing-method Class "snp.coding"
[,snp.data,ANY,ANY,ANY-method Class "snp.data"
[,snp.mx,ANY,ANY,ANY-method Class "snp.mx"
[,snp.strand,ANY,missing,missing-method Class "snp.strand"