R: genome-wide SNP association analysis

genome-wide SNP association analysis

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

GenABEL-package GenABEL: an R package for Genome Wide Association Analysis...

-- A --

add.phdata Adds phenotypic variables to gwaa...
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 arrange_probabel_phe
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
chi2_CG Detecting rare recessive and compound heterozygote alleles in genome wide association.
chromosome Class "snp.data"
chromosome-method Class "scan.gwaa"
chromosome-method Class "snp.data"
cocohet Detecting rare recessive and compound heterozygote alleles in genome wide association.
coding Class "snp.data"
coding-method Class "scan.gwaa"
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
ge03d2 GWA-type data on few small region
ge03d2.clean GWA-type data on few small region
ge03d2c GWA-type data on few small region
ge03d2ex GWA-type data on few small region
ge03d2ex.clean GWA-type data on few small region
GenABEL GenABEL: an R package for Genome Wide Association Analysis...
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 Approximate score test for association in related people
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 impute2databel
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 mach2databel
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
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...
pop2.ids GWA-type data on few small region

-- Q --

qc.nostr GWA-type data on few small region
qc.str GWA-type data on few small region
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
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"
srdta GWA-type data on small region
sset Internal use function for class snp.mx-class
strand Class "snp.data"
strand-method Class "scan.gwaa"
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

-- 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"