qtlview: Visualization of QTL Scans for Multiple Traits

Description Usage Arguments Details See Also Examples

Profiles of one or more phenotypes. If only one phenotype, in addition profile the means by genotype.

transcript.plot(cross.name, ...)
myplot(traitnames, chr = c(1:19, "X"), add = TRUE,
 title, col = c("black", "blue", "red", "green", "purple", "magenta"),
 sex, log10 = FALSE, previous = FALSE,
 model = c("normal", "binary", "2part", "np"),
 method = "hk", means = c("add", "only", "none"),
 snpgrid = 30, threshold = 0.05, n.perm = 0, ylim,
 cross.name = "B6BTBR07", legend = TRUE, ...)

`traitnames`	Character string of trait names. Can be partial match.
`chr`	Chromosomes to profile.
`add`	Add all traits to one plot if `TRUE`.
`title`	Title for LOD profile plot.
`col`	Colors for LOD profile plot.
`sex`	Character string corresponding to `traitnames`. See details.
`log10`	Transform by `log10` if `TRUE`.
`previous`	Plot on previous plot if `TRUE`.
`model`	Model argument for `scanone`.
`method`	Method argument for `scanone`.
`newdata`	New data frame to add phenotypes to cross. See details.
`covariates`	Character string of covariate names. See details.
`means`	Add means profile if `"add"`; only show means profile if `"only"`; no means profile if `"none"`.
`means.by.sex`	Separate profiles of means by sex if `TRUE` and `sex="both"`.
`lods.by.sex`	Add male and female LOD profiles if `sex="both"` and only one trait.
`title.means`	Title for means profile plot(s).
`snpgrid`	Number of ticks on SNP Mb grid.
`threshold`	Threshold p-value for permutation test.
`n.perm`	Number of permutations; none if `n.perm` = 0.
`ylim`	Limits for vertical axis on LOD profile; default to range of values across traits.
`cross.name`	Name of cross.
`legend`	Include legend if `TRUE`.
`...`	Further arguments to `scanone`.

transcript.plot is a version that is used explicitly for transcript gene mapping, or eQTL.

The sex option can be "both", "male", "female" or "ignore". With "both", Sex is included as an interacting covariate. If in addition there is only one trait, then plots for male and female are overlaid if lods.by.sex is TRUE.

New phenotypes can be added by passing a data frame with newdata. This data frame must have MouseNum as the first column, with entries Mousemmmm as IDs. Other columns must be labeled with valid R names (no special characters). Those names may be used as phenotypes or covariates. Covariates except Sex are used as additive covariates only.

B6BTBR07