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 |
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 |
blurGenotype | blur genotype calls into probabilites |
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 |
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 |
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 |
findRelatives | guesses relations between individuals |
formetascore | function to run GWA analysis oriented for future meta-analysis |
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" |
hom | function to compute average homozygosity within a person |
hom.old | 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 |
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 |
lambda | Class "scan.gwaa" |
lambda-method | Class "scan.gwaa" |
load.gwaa.data | function to load GWAA data |
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 |
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" |
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 |
qtscore | Fast score test for association |
qvaluebh95 | Computes Benjamini-Hochberg (95) q-value |
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 |
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 |
VIFGC | Genomic control for various model of inheritance using VIF |
VIFGC_ovdom | Genomic control for over-dominant model of inheritance using VIF |
Xfix | function to set impossible genotypes as missing |
ztransform | Transformation to standard Normal |
[-method | Class "gwaa.data" |
[-method | Class "scan.gwaa" |
[-method | Class "snp.coding" |
[-method | Class "snp.data" |
[-method | Class "snp.mx" |
[-method | Class "snp.strand" |