## ----include=FALSE-------------------------------------------------------
library(knitr)
opts_chunk$set(
concordance=TRUE
)
## ----load.pkg------------------------------------------------------------
library(RVPedigree)
## ----load.pheno----------------------------------------------------------
pheno.file <- system.file("extdata", "pheno.dat",
package="RVPedigree")
pheno.table <- read.table(pheno.file, header=FALSE)
dim(pheno.table)
pheno <- pheno.table[, 1]
head(pheno)
## ----load.covar----------------------------------------------------------
covar.file <- system.file("extdata", "covariates.dat",
package="RVPedigree")
covar <- as.matrix(read.table(covar.file, header=FALSE))
dim(covar)
## ----load.kinmat---------------------------------------------------------
kinship.file <- system.file("extdata", "kinmat.Rdata",
package="RVPedigree")
load(kinship.file)
dim(kin1)
rel.mat <- 2 * kin1
## ----relmat.pedigree.ped, eval=FALSE-------------------------------------
# rel.mat.pedigree.ped <- GetRelMatrix(datatype="pedigree",
# plinkbasefile="mypedfile")
## ----relmat.gen.ped, eval=FALSE------------------------------------------
# rel.mat.genomic.ped <- GetRelMatrix(datatype="genomic",
# path2Plink="/tools/genepi/Plink_1.90/plink",
# plinkbasefile="mypedfile")
## ----relmat.pedigree.bed, eval=FALSE-------------------------------------
# rel.mat.pedigree.bed <- GetRelMatrix(datatype="pedigree",
# is.binary=TRUE,
# plinkbasefile="mybedfile")
## ----relmat.gen.bed, eval=FALSE------------------------------------------
# rel.mat.genomic.bed <- GetRelMatrix(datatype="genomic",
# path2Plink="plink_1.90",
# is.binary=TRUE,
# plinkbasefile="mybedfile")
## ----load.kinmat-GenABEL-------------------------------------------------
genabel.data <- system.file("extdata", "gwaa.data.RData",
package="RVPedigree")
library(GenABEL)
load(genabel.data)
nsnps(data1)
nids(data1)
## ----compute.kinmat-GenABEL, eval=FALSE----------------------------------
# rel.mat.large <- GetRelMatrix("genomic", gwaa.data=data1)
## ----load.map------------------------------------------------------------
map.file <- system.file("extdata", "test.map",
package="RVPedigree")
mymap <- readMapFile(map.file)
## ----set.genofile--------------------------------------------------------
geno.file <- system.file("extdata", "test.ped",
package="RVPedigree")
## ----ASKAT.region--------------------------------------------------------
askat.result <- ASKAT.region(y=pheno, X=covar, Phi=rel.mat,
type="ped",
filename=geno.file,
chr=20,
startpos=0,
endpos=10000000,
map=mymap,
regionname="Gene 1")
print(askat.result)
## ----compute.kinmat-eigenv-----------------------------------------------
relmat.eig <- eigen(rel.mat)
relmat.eigvec <- relmat.eig$vectors
relmat.eigval <- relmat.eig$values
## ----NASKAT.region-------------------------------------------------------
nASKAT.result <- NormalizedASKAT.region(y=pheno, X=covar, Phi=rel.mat,
type="ped",
filename=geno.file,
chr=20,
startpos=0,
endpos=10000000,
map=mymap,
regionname="Gene 1",
U=relmat.eigvec,
S=relmat.eigval)
print(nASKAT.result)
## ----VCC1.region---------------------------------------------------------
vcc1.result <- VCC1.region(y=pheno, X=covar, Phi=rel.mat,
type="ped",
filename=geno.file,
chr=20,
startpos=0,
endpos=10000000,
map=mymap,
regionname="Gene 1")
print(vcc1.result)
## ----VCC2.region---------------------------------------------------------
vcc2.result <- VCC2.region(y=pheno, X=covar, Phi=rel.mat,
type="ped",
filename=geno.file,
chr=20,
startpos=0,
endpos=10000000,
map=mymap,
regionname="Gene 1")
print(vcc2.result)
## ----VCC2.region-perm----------------------------------------------------
vcc2.result <- VCC2.region(y=pheno, X=covar, Phi=rel.mat,
type="ped",
filename=geno.file,
chr=20,
startpos=0,
endpos=10000000,
map=mymap,
regionname="Gene 1",
Nperm=500)
print(vcc2.result)
## ----VCC3.region---------------------------------------------------------
vcc3.result <- VCC3.region(y=pheno, X=covar, Phi=rel.mat,
type="ped",
filename=geno.file,
chr=20,
startpos=0,
endpos=10000000,
map=mymap,
regionname="Gene 1")
print(vcc3.result)
## ----VCC3.region-perm----------------------------------------------------
vcc3.result <- VCC3.region(y=pheno, X=covar, Phi=rel.mat,
type="ped",
filename=geno.file,
chr=20,
startpos=0,
endpos=10000000,
map=mymap,
regionname="Gene 1",
Nperm=200)
print(vcc3.result)
## ----load.genelist-------------------------------------------------------
genes.file <- system.file("extdata", "genes2.lst",
package="RVPedigree")
genes <- read.table(genes.file,
header=TRUE,
stringsAsFactors=FALSE)
genes
colnames(genes) <- c("Name", "Chr", "StartPos", "EndPos")
## ----RVPedigree----------------------------------------------------------
gwresults <- RVPedigree(method="VCC1",
y=pheno,
X=covar,
Phi=rel.mat,
regions=genes,
filename=geno.file,
type='ped',
pvalThreshold=1
)
gwresults
## ----RVPedigree-VCC3VCC1-------------------------------------------------
gwresults <- RVPedigree(method="VCC1",
y=pheno,
X=covar,
Phi=rel.mat,
regions=genes,
filename=geno.file,
type='ped',
Nperm=200,
pvalThreshold=0.4,
VCC3afterVCC1=TRUE
)
gwresults
## ----VCC2.region-parallel------------------------------------------------
vcc2.result <- VCC2.region(y=pheno, X=covar, Phi=rel.mat,
type="ped",
filename=geno.file,
chr=20,
startpos=0,
endpos=10000000,
map=mymap,
regionname="Gene 1",
Nperm=500,
Ncores=2)
print(vcc2.result)
## ----RVPedigree-parallel-------------------------------------------------
gwresults <- RVPedigree(method="VCC1",
y=pheno,
X=covar,
Phi=rel.mat,
regions=genes,
filename=geno.file,
type='ped',
Ncores=2,
pvalThreshold=1
)
gwresults
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