getLODMatrix: Get LOD matrix.
In gact/shmootl: QTL Analysis Utilities for Yeast

Description Usage Arguments Value References See Also

Given a scantwo object, this function extracts a LOD matrix, in which the upper and lower triangle contain LOD values of a type specified by the parameters upper and lower, respectively. The method used to obtain derived LOD values is that of R/qtl function plot.scantwo (Broman et al. 2003).

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getLODMatrix(x, chr = NULL, incl.markers = FALSE, lodcolumn = NULL,
  lower = c("full", "cond-int", "int", "cond-add", "add"), upper = c("add",
  "cond-add", "int", "cond-int", "full"))

`x`	An R/qtl `scantwo` object.
`chr`	Vector indicating which sequences to include in the LOD matrix.
`incl.markers`	When `scantwo` has been run with a fixed non-zero step width, this indicates if markers (as distinct from pseudomarkers) should be included in the returned LOD matrix.
`lodcolumn`	In a `scanone` or equivalent object, this parameter indicates which LOD column to consider. In other objects with LOD-column-associated elements, this parameter indicates which LOD-column-associated element to consider. This must be either a LOD column name or an index with respect to the set of LOD columns. If no LOD column is specified and one such column is found, that column is used by default; otherwise a LOD column must be specified.
`lower`	Type of LOD score to put in the lower triangle of the LOD matrix.
`upper`	Type of LOD score to put in the upper triangle of the LOD matrix.