Description Usage Arguments Value Examples
View source: R/polyqtlR_functions.R
Function to run a single marker regression using marker dosages
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dosage_matrix |
An integer matrix with markers in rows and individuals in columns. All markers in this matrix will be tested for association with the trait. |
Phenotype.df |
A data.frame containing phenotypic values |
genotype.ID |
The colname of |
trait.ID |
The colname of |
maplist |
Option to include linkage map in the format returned by |
perm_test |
Logical, by default |
N_perm |
Integer. The number of permutations to run if |
alpha |
Numeric. The P-value to be used in the selection of a threshold if |
ncores |
Number of cores to use if parallel processing required. Works both for Windows and UNIX (using |
return_R2 |
Should the (adjusted) R2 of the model fit also be determined? |
log |
Character string specifying the log filename to which standard output should be written. If |
A list containing the following components:
QTL.res : The -log(p) of the model fit per marker are returned as "LOD" scores, although "LOP" would have been a better description. If requested, R2 values are also returned in column "R2adj"
Perm.res : The results of the permutation test if performed, otherwise NULL
Map : The linkage map if provided, otherwise NULL
1 2 3 | data("SNP_dosages.4x","BLUEs.pheno")
Trait_1.smr <- singleMarkerRegression(dosage_matrix = SNP_dosages.4x,
Phenotype.df = BLUEs.pheno,genotype.ID = "Geno",trait.ID = "BLUE")
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