genome-wide SNP association analysis


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Documentation for package `GenABEL' version 1.1-8

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GenABEL-package GenABEL: an R package for Genome Wide Association Analysis
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.data Attempts to convert snp.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.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"
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.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"
convert.snp.ped function to convert genotypic data in pre-makeped linkage fromat (+map) to internal genotypic data formated file
convert.snp.text function to convert integer genotypic data file to raw internal data formated file
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
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
ge03d2 GWA-type data on small region
ge03d2c GWA-type data on small region
ge03d2ex GWA-type data on small region
GenABEL GenABEL: an R package for Genome Wide Association Analysis
gwaa.data-class Class "gwaa.data"
hom function to compute average homozygosity within a person
HWE.show show HWE tables
ibs Computes (average) Idenity-by-State for a set of people and markers
load.gwaa.data function to load GWAA data
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
qtscore Fast score test for association
qvaluebh95 Computes Benjamini-Hochberg (95) q-value
redundant function to do redundancy check
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.data-method Class "snp.data"
show,snp.mx-method Class "snp.mx"
show.ncbi Shows the region on NCBI map
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.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
Xfix function to set heterozygous male X-linked genotypes to NA
[,gwaa.data-method Class "gwaa.data"
[,snp.data-method Class "snp.data"
[,snp.mx-method Class "snp.mx"