scanQtl: Make a QTL scan

In tavareshugo/MagicHelpR: QTL mapping in Arabidopsis MAGIC lines

Description

Make a QTL scan

Usage

scanQtl(x, phenotype, covariates = NULL, marker_cov = NULL, h1 = NULL,
  h0 = NULL, perm = 0, method = c("probability", "allele"), cores = 1)

## S4 method for signature 'MagicGenPhen'
scanQtl(x, phenotype, covariates = NULL,
  marker_cov = NULL, h1 = NULL, h0 = NULL, perm = 0,
  method = c("probability", "allele"), cores = 1)

Arguments

x	an object of class MagicGenPhen
phenotype	to run QTL analysis on.
covariates	optional name of column(s) from phenotypes to use as covariate(s). Default: NULL
marker_cov	optional ID of marker(s) to use as covariate(s) in the model. Default: NULL
h1	optional optional model to test. Need to provide 'h0' as well. Default: NULL
h0	optional optional null model to test against. Need to provide 'h1' as well. Default: NULL
perm	optional number of permutations to run. If provided will permute the phenotypes the number of requested times and then run the QTL scan. It will add a new column to the output with a genome-wide p-value (proportion of times where observed p > permuted p). Default: 0
method	the method to incorporate genotypes in the model. Either "probability", which uses probability matrices of founder ancestry for each marker or "allele" to simply use the marker alleles (typically two alleles from a SNP). Default: probability.
cores	number of cores to use (Windows only supports 1 core). Default: 1

Value

a data.frame with the QTL results.

Examples

# to be added...

tavareshugo/MagicHelpR documentation built on May 4, 2020, 3:01 p.m.