View source: R/QTL_betaBinomial.R
QTL_BetaBin
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MeRIPdata |
The MeRIP.Peak object |
vcf_file |
The vcf file for genotype. The chromosome position must be sorted!! |
BSgenome |
The BSgenome object. This needs to match the genome version of the gtf files. |
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. |
AdjustGC |
Logic. Choose whether explicitly adjust GC bias. |
AdjIPeffi |
Logic. Choose whether explicitly adjust overall IP efficiency |
normalizeGenotype |
Logic. Choose whether genotype is normalized to mean = 0, var = 1 before regression. |
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