/usr/lib/R/site-library/GenABEL/INDEX is in r-cran-genabel 1.7-6-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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GC Genomic control for various model of
inheritance using VIF
GC_ovdom Genomic control for overdimunant model of
inheritance using VIF
GenABEL GWAS in R
HWE.show show HWE tables
PGC Polynomial genomic control
Xfix function to set impossible genotypes as missing
add.phdata Adds phenotypic variables to gwaa.data object
add.plot function to plot additional GWAA results
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
cocohet Test for compound heterozygote effects
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
dprfast Estimates D' between multiple markers
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
ge03d2 GWA-type data on few small region
generateOffspring simulates offspring's genotypes
getLogLikelihoodGivenRelation
computes logLik of two blurGenotypes
grammar GRAMMAR test for association in samples with
genetic structure
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
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
impute2databel converts IMPUTE-imputed files to DatABEL
(filevector) format
impute2mach converts IMPUTE to MACH files
load.gwaa.data function to load GWAA data
mach2databel converts MACH-imputed files to DatABEL
(filevector) format
makeTransitionMatrix Genotype transition probabilities matrices
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
npsubtreated non-parametric trait "imputations" in treated
people
patch_strand function to change strand
perid.summary Summary of marker data per person
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
refresh.gwaa.data Updates an object from old to new GenABEL
format
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.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
snps.cell-class Class "snps.cell"
sortmap.internal Internal function for map-sorting
srdta GWA-type data on small region
sset Internal use function for class snp.mx-class
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
ztransform Transformation to standard Normal
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