R: genome-wide SNP association analysis

# genome-wide SNP association analysis

## Documentation for package ‘GenABEL’ version 1.8-0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.

## Help Pages

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

GenABEL-package | GWAS in R

## -- A --

add.phdata | Adds phenotypic variables to gwaa.data object
add.plot | function to plot additional GWAA results
annotation | Class "snp.data"
annotation-method | Class "scan.gwaa"
annotation-method | Class "snp.data"
arrange_probabel_phe | arranges ProbABEL phenotype-file
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

## -- B --

blurGenotype | blur genotype calls into probabilites

## -- 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
checkPackageVersionOnCRAN | checks what is the version of package on CRAN
chi2_CG | Test for compound heterozygote effects
chromosome | Class "snp.data"
chromosome-method | Class "scan.gwaa"
chromosome-method | Class "snp.data"
cocohet | Test for compound heterozygote effects
coding | Class "snp.data"
coding-method | Class "scan.gwaa"
coding-method | Class "snp.data"
coding<- | Class "snp.data"
coding<--method | Class "snp.data"
coerce-method | Class "snp.coding"
coerce-method | Class "snp.data"
coerce-method | Class "snp.mx"
coerce-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 --

del.phdata | delete phenotypes from phdata
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
dim-method | Class "scan.gwaa"
dim-method | Class "snp.data"
dimnames-method | Class "scan.gwaa"
dimnames-method | Class "snp.data"
dprfast | Estimates D' between multiple markers

## -- E --

effallele | Class "snp.data"
effallele-method | Class "scan.gwaa"
effallele-method | Class "snp.data"
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.impute | function to export GenABEL data in IMPUTE format
export.merlin | function to export GenABEL data in merlin format
export.plink | Export GenABEL data in PLINK format
extract.annotation.impute | extracts SNP annotation from IMPUTE files
extract.annotation.mach | extracts SNP annotation from MACH/HapMap legend files

## -- F --

findRelatives | guesses relations between individuals
formetascore | function to run GWA analysis oriented for future meta-analysis

## -- G --

GASurv | Makes survival data object for reg.gwaa
GenABEL | GWAS in R
genabel | GWAS in R
generateOffspring | simulates offspring's genotypes
getcall | Class "scan.gwaa"
getcall-method | Class "scan.gwaa"
getfamily | Class "scan.gwaa"
getfamily-method | Class "scan.gwaa"
getLogLikelihoodGivenRelation | computes logLik of two blurGenotypes
grammar | GRAMMAR test for association in samples with genetic structure
gtdata | Class "gwaa.data"
gtdata-method | Class "gwaa.data"
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
idnames | Class "snp.data"
idnames-method | Class "scan.gwaa"
idnames-method | Class "snp.data"
impute2databel | converts IMPUTE-imputed files to DatABEL (filevector) format
impute2mach | converts IMPUTE to MACH files

## -- L --

lambda | Class "scan.gwaa"
lambda-method | Class "scan.gwaa"
load.gwaa.data | function to load GWAA data

## -- M --

mach2databel | converts MACH-imputed files to DatABEL (filevector) format
makeTransitionMatrix | Genotype transition probabilities matrices
male | Class "snp.data"
male-method | Class "scan.gwaa"
male-method | Class "snp.data"
map | Class "snp.data"
map-method | Class "scan.gwaa"
map-method | Class "snp.data"
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 --

nids | Class "snp.data"
nids-method | Class "scan.gwaa"
nids-method | Class "snp.data"
npsubtreated | non-parametric trait "imputations" in treated people
nsnps | Class "snp.data"
nsnps-method | Class "scan.gwaa"
nsnps-method | Class "snp.data"

## -- P --

patch_strand | function to change strand
perid.summary | Summary of marker data per person
PGC | Polynomial genomic control
phdata | Class "gwaa.data"
phdata-method | Class "gwaa.data"
phdata<- | Class "gwaa.data"
phdata<--method | Class "gwaa.data"
plot-method | Class "check.marker"
plot-method | Class "scan.gwaa"
plot-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
polygenic_hglm | Estimation of polygenic model

## -- Q --

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
recodeChromosome | Change chromosomal coding
reconstructNPs | reconstruct nuclear families
redundant | function to do redundancy check
refallele | Class "snp.data"
refallele-method | Class "scan.gwaa"
refallele-method | Class "snp.data"
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
results | Class "scan.gwaa"
results-method | Class "scan.gwaa"
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-method | Class "gwaa.data"
show-method | Class "scan.gwaa"
show-method | Class "snp.coding"
show-method | Class "snp.data"
show-method | Class "snp.mx"
show-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
snpnames | Class "snp.data"
snpnames-method | Class "scan.gwaa"
snpnames-method | Class "snp.data"
snps.cell-class | Class "snps.cell"
sortmap.internal | Internal function for map-sorting
sset | Internal use function for class snp.mx-class
strand | Class "snp.data"
strand-method | Class "scan.gwaa"
strand-method | Class "snp.data"
strand<- | Class "snp.data"
strand<--method | Class "snp.data"
summary-method | Class "check.marker"
summary-method | Class "gwaa.data"
summary-method | Class "snp.data"
summary-method | Class "snp.mx"
summary.check.marker | Summary of check.marker object
summary.gwaa.data | function to summarise GWAA data
summary.scan.gwaa | Shortcut to 'descriptives...
summary.snp.data | function to summary GWAA data
summary.snp.data_old | function to summary GWAA data

## -- V --

VIFGC | Genomic control for various model of inheritance using VIF
VIFGC_ovdom | Genomic control for over-dominant model of inheritance using VIF

## -- X --

Xfix | function to set impossible genotypes as missing

## -- Z --

ztransform | Transformation to standard Normal

## -- misc --

[-method | Class "gwaa.data"
[-method | Class "scan.gwaa"
[-method | Class "snp.coding"
[-method | Class "snp.data"
[-method | Class "snp.mx"
[-method | Class "snp.strand"