make_htrx {HTRX}

Generate haplotype data

Description

Generate the feature data, either the genotype data for single nucleotide polymorphisms (SNPs) (make_snp), the feature data for Haplotype Trend Regression (HTR) (make_htr), or the feature data for Haplotype Trend Regression with eXtra flexibility (HTRX) (make_htrx).

Usage

make_htrx(
  hap1,
  hap2 = hap1,
  rareremove = FALSE,
  rare_threshold = 0.001,
  fixedfeature = NULL,
  max_int = NULL
)

make_htr(hap1, hap2 = hap1, rareremove = FALSE, rare_threshold = 0.001)

make_snp(hap1, hap2 = hap1, rareremove = FALSE, rare_threshold = 0.001)

Arguments

hap1

a data frame of the SNPs' genotype of the first genome. The genotype of a SNP for each individual is either 0 (reference allele) or 1 (alternative allele).

hap2

a data frame of the SNPs' genotype of the second genome. The genotype of a SNP for each individual is either 0 (reference allele) or 1 (alternative allele). By default, hap2=hap1 representing haploid.

rareremove

logical. Remove rare SNPs and haplotypes or not. By default, rareremove=FALSE.

rare_threshold

a numeric number below which the haplotype or SNP is removed. This only works when rareremove=TRUE. By default, rare_threshold=0.001.

fixedfeature

a character consisted of the names of haplotypes. This parameter can be NULL (by default) if all the haplotypes are used as variables.

max_int

a positive integer which specifies the maximum number of SNPs that can interact. If no value is given, interactions between all the SNPs will be considered.

Details

If there are n SNPs, there are 2ⁿ different haplotypes created by HTR, and 3ⁿ-1 different haplotypes created by HTRX.

When the data is haploid, please use the default setting hap2=hap1.

Value

a data frame of the feature data (either for SNPs, HTR or HTRX).

Examples

## create SNP data for both genomes (diploid data)
hap1=as.data.frame(matrix(0,nrow=100,ncol=4))
hap2=as.data.frame(matrix(0,nrow=100,ncol=4))
colnames(hap1)=colnames(hap2)=c('a','b','c','d')
p=runif(4,0.01,0.99)
for(j in 1:4){
  hap1[,j]=rbinom(100,1,p[j])
  hap2[,j]=rbinom(100,1,p[j])
}

## create the SNP data without removing rare SNPs
make_snp(hap1,hap2)

## create feature data for "HTR" removing haplotypes rarer than 0.5%
make_htr(hap1,hap2,rareremove=TRUE,0.005)

## create feature data for "HTRX"
## retaining haplotypes with interaction across at most 3 SNPs
make_htrx(hap1,hap2,max_int=3)

## create feature data for feature "01XX" and "X101"
## without removing haplotypes
make_htrx(hap1,hap2,fixedfeature=c("01XX","X101"))

## If the data is haploid instead of diploid
## create feature data for "HTRX" without removing haplotypes
make_htrx(hap1,hap1)