Description Usage Arguments Value References See Also
Run qtl::scanone
on a single permuted cross
object.
1 2 |
perm.id |
Permutation index. |
cross |
An R/qtl |
pheno.col |
Phenotype columns for which QTL analysis should be run. If no phenotypes are specified, all are used. |
perm.pheno |
Permute phenotype data. |
perm.geno |
Permute genotype data. |
perm.type |
Type of permutation data to return (see below). |
... |
Additional keyword arguments passed to |
If perm.type
is set to 'max'
, a regular
scanoneperm
object is returned, containing the maximum
LOD value from the given permutation. If perm.type
is
set to 'bins'
, a scanonebins
array is returned.
The single row of this array corresponds to the permutation,
each column corresponds to a bin spanning an interval of LOD
values, and each slice corresponds to a LOD column. Each array
element contains the number of loci in the given bin interval
for that LOD column in that permutation.
Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889-890. (PubMed)
Other scan utility functions: batchPermScanoneF
,
batchPermScanone
,
batchPermScantwoF
,
batchPermScantwo
,
batchPhenoScanone
,
batchPhenoScantwo
, batchScan
,
nodePermScanoneF
,
nodePermScantwoF
,
nodePermScantwo
,
nodePhenoScanone
,
nodePhenoScantwo
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