DSPRscan: DSPR Genome Scan
In egking/DSPRqtl: Analysis of DSPR phenotypes in R

Description Usage Arguments Value Author(s)

Function to perform a genome scan for data generated with the DSPR RILs. This function is capable of fitting standard models. Users requiring more flexibility should use the DSPRgenos function along with standard model fitting functions in R.

1	DSPRscan(model, design, phenotype.dat, id.col, batch = 1000, sex)

`model`	an object of class formula: a symbolic description of the null model to be fitted at each position (e.g., `phenotype ~ 1`). The genotype effects to be fitted will be added based on `design`.
`design`	a character string. One of either 'inbredA', 'inbredB', or 'ABcross' corresponding to the pA and pB set of inbred RILs or the pA-pB cross design. For round robin designs or other cross designs, use the more flexible DSPRgenos and standard model fitting functions in R.
`phenotype.dat`	`data.frame` containing phenotype data. For inbred designs, there must be a column of numeric RIL ids (must be named patRIL). For the ABcross design, there must be both a patRIL and matRIL column specifying the pA and pB RIL ids.
`id.col`	a character string identifying the name of the column containing unique ids for the samples. e.g. for an inbred design, the patRIL column can be used as the id.
`batch`	A numeric vector of length one specifying the number of positions to be examined at a time. A larger number will use more memory but can be faster. Default is 1000.
`sex`	a character string (either 'm' or 'f') specifying the sex of the measured individuals. This argument must be supplied for a cross design for correct specification of the genotypes on the X chromosome.

A list of class gscan containing:

`LODscores`	A `data.frame` consisting of the chromosome, physical position (bp), genetic position (cM) and LOD score for each position.
`model`	the model specification
`design`	the design specification
`phenotype`	the phenotype `data.frame` specified