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" |