View source: R/QTL_PoissonGamma.R
1 2 | QTL_PoissonGamma(pheno, vcf_file, peak_bed, testWindow = 1e+05, Chromosome,
Range = NULL, Covariates = NULL, maxPsi = 100, thread = 1)
|
pheno |
The phenotype data matrix. Needs to be IP read count that has been normalized for expression level. |
vcf_file |
The vcf file for genotype. The chromosome position must be sorted!! |
peak_bed |
The peak file in BED12 format that needs to correspond to phenotype data matrix. |
testWindow |
Integer. Test SNPs in <testWindow> bp window flanking the peak. |
Chromosome |
The chromsome to run QTL test. |
Range |
The position range on a chromosome to test. |
Covariates |
The matrix for covariates to be included in the test. |
maxPsi |
The max estimation for the random effect parameter Psi. |
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