Man pages for GenABEL
genome-wide SNP association analysis

add.phdataAdds phenotypic variables to object
add.plotfunction to plot additional GWAA results
arrange_probabel_phearranges ProbABEL phenotype-file
as.character.gwaa.dataAttempts to convert genotypic part of to character
as.character.snp.codingAttempts to convert internal snp.coding-class to character
as.character.snp.dataAttempts to convert to character
as.character.snp.strandAttempts to convert internal strand-class to character to convert to "hsgeno"
as.double.gwaa.dataAttempts to convert to double
as.double.snp.dataAttempts to convert to double
as.genotypeAttempts to convert object to "genotype"
as.genotype.gwaa.dataAttempts to convert to "genotype"
as.genotype.snp.dataAttempts to convert to "genotype"
as.hsgenoAttempts to convert object to "hsgeno"
as.hsgeno.gwaa.dataAttempts to convert to "hsgeno"
as.hsgeno.snp.dataAttempts to convert to "hsgeno"
autosomalFunction telling all autosomal SNPs
blurGenotypeblur genotype calls into probabilites
catablefunction to generate summary table for quantitative data
ccfastfast case-control analysis
check.markerfunction to do genotypic quality control
check.marker-classClass "check.marker"
checkPackageVersionOnCRANchecks what is the version of package on CRAN
check.traitfunction to do primitive trait quality control
cocohetTest for compound heterozygote effects
convert.snp.affymetrixfunction to convert genotypic data from Affymetrix to...
convert.snp.illuminafunction to convert genotypic data from Illumina/Affymetrix...
convert.snp.machfunction to convert genotypic data from MACH format to...
convert.snp.pedfunction to convert genotypic data in pedigree fromat (+map)...
convert.snp.textfunction to convert integer genotypic data file to raw...
convert.snp.tpedfunction to convert genotypic data in transposed-ped format...
crnamesReturn column and row names
del.phdatadelete phenotypes from phdata
descriptives.markerFunction to generate descriptive summary tables for genotypic...
descriptives.scanFunction to describe "top" hits in GWA scan
descriptives.traitFunction to generate descriptive summary tables for...
dprfastEstimates D' between multiple markers
egscoreFast score test for association, corrected with PC
egscore.oldFast score test for association, corrected with PC
emp.ccfastGenome-wide significance for a case-control GWA scan
emp.qtscoreGenome-wide significance for a GWA scan
estlambdaEstimate the inflation factor for a distribution of P-values
export.imputefunction to export GenABEL data in IMPUTE format
export.merlinfunction to export GenABEL data in merlin format
export.plinkExport GenABEL data in PLINK format
extract.annotation.imputeextracts SNP annotation from IMPUTE files
extract.annotation.machextracts SNP annotation from MACH/HapMap legend files
findRelativesguesses relations between individuals
formetascorefunction to run GWA analysis oriented for future...
GASurvMakes survival data object for reg.gwaa
generateOffspringsimulates offspring's genotypes
getLogLikelihoodGivenRelationcomputes logLik of two blurGenotypes
grammarGRAMMAR test for association in samples with genetic... ""
homfunction to compute average homozygosity within a person
hom.oldfunction to compute average homozygosity within a person
HWE.showshow HWE tables
ibsComputes (average) Idenity-by-State for a set of people and...
ibs.oldComputes (average) Idenity-by-State for a set of people and...
impute2databelconverts IMPUTE-imputed files to DatABEL (filevector) format
impute2machconverts IMPUTE to MACH files
load.gwaa.datafunction to load GWAA data
mach2databelconverts MACH-imputed files to DatABEL (filevector) format
makeTransitionMatrixGenotype transition probabilities matrices
merge.gwaa.datafunction to merge objects of
merge.snp.datafunction to merge objects of
mlregLinear and logistic regression and Cox models for genome-wide...
mlreg.pEXPERIMENTAL Linear and logistic regression and Cox models...
mmscoreScore test for association in related people
npsubtreatednon-parametric trait "imputations" in treated people
patch_strandfunction to change strand
perid.summarySummary of marker data per person
PGCPolynomial genomic control
plot.check.markerplots "check.marker" object
plot.scan.gwaafunction to plot GWAA results
plot.scan.gwaa.2Dfunction to plot 2D scan results
polygenicEstimation of polygenic model
polygenic_hglmEstimation of polygenic model
qtscoreFast score test for association
qvaluebh95Computes Benjamini-Hochberg (95) q-value
r2fastEstimates r2 between multiple markers
r2fast.oldEstimates r2 between multiple markers
recodeChromosomeChange chromosomal coding
reconstructNPsreconstruct nuclear families
redundantfunction to do redundancy check
refresh.gwaa.dataUpdates an object from old to new GenABEL format
rhofastEstimates rho between multiple markers
rntransformRank-transformation to normality
save.gwaa.datafunction to save object
scan.glmScan GWA data using glm
scan.glm.2DScans regional data allowing for gene-gene interaction using...
scan.gwaa.2D-classClass "scan.gwaa.2D"
scan.gwaa-classClass "scan.gwaa"
scan.haplo.2Druns haplo.score.slide with all pairs of markers in a region
show.ncbiShows the region on NCBI map
snp.coding-classClass "snp.coding"
snp.datacreates an object "" ""
snp.namesextracts names of SNPs in a region
snps.cell-classClass "snps.cell"
snp.strand-classClass "snp.strand"
snp.subsetfunction to subset objects of class scan.gwaa and...
sortmap.internalInternal function for map-sorting
ssetInternal use function for class
summary.check.markerSummary of check.marker object
summary.gwaa.datafunction to summarise GWAA data
summary.scan.gwaaShortcut to 'descriptives...
summary.snp.datafunction to summary GWAA data
VIFGCGenomic control for various model of inheritance using VIF
VIFGC_ovdomGenomic control for over-dominant model of inheritance using...
Xfixfunction to set impossible genotypes as missing
ztransformTransformation to standard Normal
GenABEL documentation built on May 30, 2017, 3:36 a.m.