Make a QTL scan
scanQtl(x, phenotype, covariates = NULL, marker_cov = NULL, h1 = NULL, h0 = NULL, perm = 0, method = c("probability", "allele"), cores = 1) # S4 method for MagicGenPhen scanQtl(x, phenotype, covariates = NULL, marker_cov = NULL, h1 = NULL, h0 = NULL, perm = 0, method = c("probability", "allele"), cores = 1)
| 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 |
a data.frame with the QTL results.
# to be added...