QTL_BetaBin2: QTL_BetaBin2
In scottzijiezhang/MeRIPtools: Analyze MeRIP-seq data and QTL calling

Description Usage Arguments

Same as QTL_BetaBin except sizeFactor estimated by Median of ratio method was used to scale library size instead of total coverage.

QTL_BetaBin2(MeRIPdata, vcf_file, BSgenome = BSgenome.Hsapiens.UCSC.hg19,
  testWindow = 1e+05, Chromosome, Range = NULL, Covariates = NULL,
  AdjustGC = TRUE, PCsToInclude = 0, normalizeGenotype = FALSE,
  thread = 1)

`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.
`normalizeGenotype`	Logic. Choose whether genotype is normalized to mean = 0, var = 1 before regression.