scanqtl {qtl} | R Documentation |

Performs a multiple QTL scan for specified chromosomes and positions or intervals, with the possible inclusion of QTL-QTL interactions and/or covariates.

scanqtl(cross, pheno.col=1, chr, pos, covar=NULL, formula, method=c("imp"), incl.markers=FALSE)

`cross` |
An object of class `cross` . See
`read.cross` for details. |

`pheno.col` |
Column number in the phenotype matrix which should be used as the phenotype. |

`chr` |
Vector indicating the chromosome for each QTL. |

`pos` |
List indicating the positions or intervals on the chromosome to be scanned. Each element should be either a single number (for a specific position) or a pair of numbers (for an interval). |

`covar` |
A data frame of covariates. |

`formula` |
An object of class `formula`
indicating the model to be fitted. QTLs are indicated as `Q1` ,
`Q2` , etc. Covariates are indicated by their names in `covar` . |

`method` |
Indicates whether to use the EM algorithm or imputation. (Only imputation is implemented at this point.) |

`incl.markers` |
If FALSE, do calculations only at points on an evenly spaced grid. |

The formula is used to specified the model to be fitted. In the
formula, user has to use `Q1`

, `Q2`

, etc., or `q1`

,
`q2`

, etc., to represent the QTLs, and the column names in the
covariate data frame to represent the covariates.

Only the interaction terms need to be specifed in the formula. The
main effects of all input QTLs (as specified by chr and pos) and
covariates (as specifed by covar) will be included by default. For
example, if the formula is `y~Q1*Q2*Sex`

, there are three
elements in input chr and pos and Sex is one of the column names for
input cov, the formula used in genome scan will be
`y ~ Q1 + Q2 + Q3 + Sex + Q1:Q2 + Q1:Sex + Q2:Sex + Q1:Q2:Sex`

.

The input pos is a list or vector to specify the position/range of the input chromosomes to be scanned. If it is a vector, it gives the specified position on the chromosomes. If it is a list, it will contain either the certain positions or a range on chromosomes. For example, the input chr is c(1, 6, 13). If pos is c(9.8, 34.0, 18.6), it means to scan chromosome 1 at 9.8cM, chromosome 6 at 34cM and chromosome 13 at 18.6cM. If pos is list(c(5,15), c(30,36), 18), it means to scan chromosome 1 from 5cM to 15cM, chromosome 6 from 30cM to 36cM, fix chromosome 13 at 18cM.

An object of class `scanqtl`

. It is a multi-dimensional
array of LOD scores, with the number of dimension equal to the number
of QTLs specifed.

Hao Wu, hao@jax.org

Sen, S. and Churchill, G. A. (2001) A statistical framework for quantitative
trait mapping. *Genetics* **159**, 371–387.

data(fake.f2) # take out several QTLs qc <- c(1, 8, 13) fake.f2 <- subset(fake.f2, chr=qc) # imputate genotypes # 2-dimensional genome scan with additive 3-QTL model pos <- list(c(15,35), c(45,65), 28) result <- scanqtl(fake.f2, pheno.col=1, chr=qc, pos=pos, formula=y~Q1+Q2+Q3) # image of the results # chr locations chr1 <- as.numeric(matrix(unlist(strsplit(colnames(result),"@")), ncol=2,byrow=TRUE)[,2]) chr8 <- as.numeric(matrix(unlist(strsplit(rownames(result),"@")), ncol=2,byrow=TRUE)[,2]) # image plot image(chr1, chr8, t(result), las=1, col=rev(rainbow(256,start=0,end=2/3))) # do the same, allowing the QTLs on chr 1 and 13 to interact result2 <- scanqtl(fake.f2, pheno.col=1, chr=qc, pos=pos, formula=y~Q1+Q2+Q3+Q1:Q3) # image plot image(chr1, chr8, t(result2), las=1, col=rev(rainbow(256,start=0,end=2/3)))

[Package *qtl* version 0.98-57 Index]