fourierExpansion: Fourier Expansion of Genotype
In FRGEpistasis: Epistasis Analysis for Quantitative Traits by Functional Regression Model
Description
Usage
Arguments
Details
Value
Author(s)
Examples
View source: R/fourierExpansion.R
Description
This function aims to expand the genotype of one gene (or genomic region)
with Fourier Expansion.
Usage
1
fourierExpansion(gene_idx, geno, gene_list, snp_map, rng)
Arguments
gene_idx
The expansion gene index in the gene annotation list.
geno
Genotype of all the genes in the gene annotation list.
gene_list
Gene annotation list which includes gene name, chromosome, start position and end position.
snp_map
SNP genetic map includes chromosome, snp indentifier, genetic distance and base-pair position.
rng
A numeric value which represents gene region extensible scope.
Details
This function reduces the dimension of one gene(or genomic region) with Fourier Expansion.
Fist extract out the genotype of this gene with the gene annotation and the SNP map information.
Then expanse the gene with the genotypes and SNP positions if the number of SNPs in the gene is over 3.
Otherwise the raw genotypes of the gene would be returned.
The number of Fourier Basis is selected to explain 80 percent of genetic variation.
Value
If the SNPs number of the gene is over 3, returns the expansion of the genotype which is a matrix
with the dimension Sample number * Fourier Basis number.
If the SNPs number of the gene is no more than 3, returns the raw genotype of the gene which is a matrix
with the dimension Sample number * SNP number.
Author(s)
Futao Zhang
Examples
1
2
3
4
5
gLst<-read.csv(system.file("extdata", "gene.list.csv", package="FRGEpistasis"))
fdata<-read.table(system.file("extdata", "simGeno-chr1.raw", package="FRGEpistasis"),header=TRUE)
geno<-fdata[,-1:-6]
snp_map<-read.table(system.file("extdata", "chr1.map", package="FRGEpistasis"))
fourierExpansion(1, geno, gLst, snp_map, 0)
Example output
Loading required package: MASS
Loading required package: fda
Loading required package: splines
Loading required package: Matrix
Attaching package: 'fda'
The following object is masked from 'package:graphics':
matplot
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FRGEpistasis documentation built on Nov. 8, 2020, 5:51 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value Author(s) Examples
View source: R/fourierExpansion.R
Description
This function aims to expand the genotype of one gene (or genomic region) with Fourier Expansion.
Usage
1 | fourierExpansion(gene_idx, geno, gene_list, snp_map, rng)
|
Arguments
gene_idx |
The expansion gene index in the gene annotation list. |
geno |
Genotype of all the genes in the gene annotation list. |
gene_list |
Gene annotation list which includes gene name, chromosome, start position and end position. |
snp_map |
SNP genetic map includes chromosome, snp indentifier, genetic distance and base-pair position. |
rng |
A numeric value which represents gene region extensible scope. |
Details
This function reduces the dimension of one gene(or genomic region) with Fourier Expansion. Fist extract out the genotype of this gene with the gene annotation and the SNP map information. Then expanse the gene with the genotypes and SNP positions if the number of SNPs in the gene is over 3. Otherwise the raw genotypes of the gene would be returned. The number of Fourier Basis is selected to explain 80 percent of genetic variation.
Value
If the SNPs number of the gene is over 3, returns the expansion of the genotype which is a matrix with the dimension Sample number * Fourier Basis number. If the SNPs number of the gene is no more than 3, returns the raw genotype of the gene which is a matrix with the dimension Sample number * SNP number.
Author(s)
Futao Zhang
Examples
1 2 3 4 5 | gLst<-read.csv(system.file("extdata", "gene.list.csv", package="FRGEpistasis"))
fdata<-read.table(system.file("extdata", "simGeno-chr1.raw", package="FRGEpistasis"),header=TRUE)
geno<-fdata[,-1:-6]
snp_map<-read.table(system.file("extdata", "chr1.map", package="FRGEpistasis"))
fourierExpansion(1, geno, gLst, snp_map, 0)
|
Example output
Loading required package: MASS
Loading required package: fda
Loading required package: splines
Loading required package: Matrix
Attaching package: 'fda'
The following object is masked from 'package:graphics':
matplot
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