(1) UNC score test:

UNCcombo.score.test(trait,type,snp.glf, cov, snp.name=NULL)

Input:

• trait: a vector of trait values (Binary trait must take 0/1 values).
• type: "quantitative" or "binary" (for trait).
• snp.glf: Genotype Likelihood Function (GLF), which is a matrix of three columns. The three columns correspond to the values of three GLFs of a SNP. For instance, if major allele is A and minor allele is B, then the order of three GLFs is glf(AA), glf(AB),glf(BB). GLFs can be obtained using bcftools on bcf files (command line sample: bcftools view bam.raw.bcf | grep -v "#" | grep '^[1-9]' | cut -f 1,2,4,5,10- > bam.glf )
• cov: a matrix of covariates.
• snp.name (optional): name of the SNP

Output: a vector contains the SNP name (optional), the pvalue of the score test and the estimated minor allele frequency for the given SNP.

(2) UNC LRT:

UNCcombo.LRT(trait,type,snp.glf, cov, snp.name=NULL)

Input:

• trait: a vector of trait values (Binary trait must take 0/1 values).
• type: "quantitative" or "binary" (for trait).
• snp.glf: a matrix of three columns. The three columns correspond to the values of three genotype likelihood functions of a SNP. For instance, if major allele is A and minor allele is B, then the order of three GLFs is glf(AA), glf(AB),glf(BB).
• cov: a matrix of covariates.
• snp.name (optional): name of the SNP

Output: a vector contains the SNP name (optional), the pvalue of the LRT and the estimated minor allele frequency for the given SNP.

(3) UNC combo:

UNCcombo.combo(trait,type,snp.glf, cov, maf_threshold=0,snp.name=NULL)

Input:

• trait: a vector of trait values.
• type: "quantitative" or "binary" (Binary trait must take 0/1 values).
• snp.glf: a matrix of three columns. The three columns correspond to the values of three genotype likelihood functions of a SN\ P. For instance, if major allele is A and minor allele is B, then the order of three GLFs is glf(AA), glf(AB),glf(BB).
• maf_threshold: MAF threshold. Default is 0.
• cov: a matrix of covariates.
• snp.name (optional): name of the SNP

Output: a vector contains the SNP name (optional), the pvalue of the LRT and the estimated minor allele frequency for the given SNP.

Example

• Download example.dat and example.cov.
• Prepare input:
  pheno_glf<- read.table("local_path/example.dat")
  cov <- as.matrix(read.table("local_path/example.cov"))
  pheno <- pheno_glf[,1]
  glf <- pheno_glf[,-1]
  snp_num <- (ncol(pheno_glf) - 1)/3
• Output:
  #UNC score test
  score_results <- matrix(1,snp_num,2)
  for(k in 1:snp_num)
  score_results[k,] <- UNCcombo.score.test(pheno,type="binary",glf[,(3*k-2):(3*k)],cov)
  
  #UNC LRT
  lrt_results <- matrix(1,snp_num,2)
  for(k in 1:snp_num)
  lrt_results[k,] <- UNCcombo.LRT(pheno,type="binary",glf[,(3*k-2):(3*k)],cov)
  
  #UNC combo
  combo_results <- matrix(1,snp_num,2)
  for(k in 1:snp_num)
  combo_results[k,] <- UNCcombo.combo(pheno,type="binary",glf[,(3*k-2):(3*k)],cov)