binQTLScan: QTL mapping with binmap data

In venyao/binQTL: QTL mapping with binmap

Description

The phenotype data frame should contain two columns. The first column is the ID of each accession of a population. The second column contains the phenotypic value of specific trait for each accession. For RIL (recombinant Inbred lines) or F2 population, each row of the genotype data frame represents a Bin. The first column is the ID of each Bin. The second column is the chromosome ID of each Bin. The 3rd column is the start coordinate of each Bin. The 4th column is the end coordinate of each Bin. Each of the rest columns gives the genotype of each accession at different bins. The names of the rest columns can be any characters specified by the User. For MAGIC population with 8 parents, each bin should be represented as 8 lines. The population type can be RIL, F2 or magic.

Usage

   binQTLScan(phenotype="", genotype="", population="RIL")

Arguments

phenotype	A data frame representing the phenotype of a population.
genotype	A data frame representing the genotype of a population.
population	A character string indicating the type of the population.

Author(s)

Wen Yao, Shizhong Xu

Examples

  ril.phe <- read.csv(system.file("examples/ril.phe.csv", package="binQTL"), as.is=TRUE)
  dim(ril.phe)
  head(ril.phe)
  ril.geno <- read.csv(system.file("examples/ril.geno.csv", package="binQTL"), as.is=TRUE)
  dim(ril.geno)
  ril.geno[1:2, 1:9]
  qtl.res <- binQTLScan(phenotype = ril.phe, genotype = ril.geno, population="RIL")
  head(qtl.res)
  

venyao/binQTL documentation built on June 9, 2019, 4:52 a.m.