bim.effects {bim} | R Documentation |

Histogram of QTL loci plus scatter plots and smooth estimates of QTL effects (additive and dominance–Mather-Jinks model).

plot.bim.effects(x, cross, nqtl = 1, pattern = NULL, exact = FALSE, chr, bw = 2, qtl = <<see below>>, cex, level = .80, project=<<see below>>, main=<<see below>>, mfcol=<<see below>>, ... ) bim.effects(x, cross, nqtl = 1, pattern = NULL, exact = FALSE, chr, bw = 2, qtl = <<see below>>)

`x` |
object of class `bim` |

`cross` |
corresponding object of class `cross` |

`nqtl` |
subset on number of QTL |

`pattern` |
subset on chromosome pattern of QTL |

`exact` |
subset on exact pattern or number of QTL if true |

`chr` |
subset of chromosomes to plot (numerical indices or chromosome names) |

`bw` |
bandwidth for loci density |

`qtl` |
QTL estimate information (see value) |

`cex` |
character expansion for scatter plots |

`prefix` |
prefix for chromosome names, typically `c` |

`level` |
level for HPD region from `seq(.5,.95,by=.05)` |

`project` |
project identifier, default is name of `x` argument |

`main` |
title, with default ```
expression(project summaries
with m >= nqtl)
``` and substitutions for `project` and
`nqtl` |

`mfcol` |
parameter to `par` set to 2 or 3 depending on if
dominance is present |

`...` |
graphical parameters can be given as arguments to
`plot` |

Model averaging conditional on at least `nqtl`

and at least
chromosome `pattern`

QTL in model.
`bim.effects`

uses `bim.qtl`

to estimate the QTL
First row has histogram of loci overlaid with smoothed density estimate
(blue line) and HPD regions (red circles along origin).
Second row is additive effect; third if present has dominance effect.
Smoothing spline fit along scatter plot to estimate mean effects (solid
blue line), plus or minus two SDs (dashed blue line; estimated as well
by smoothing spline). Simple linear regression used if 50 or fewer
samples for a chromosome.
Purple triangles indicate marker locations if supplied. Red circles and
vertical dashed lines at estimated loci and effects. Vertical black
lines delineate chromosomes.

`bim.effects`

returns an enhanced version of the
`bim.qtl`

object, with additional elements

`add` |
additive smoothing spline by chromosome |

`dom` |
dominance smoothing spline by chromosome (if present) |

`est` |
estimates of QTL |

`chrom` |
chromosome name |

`loci` |
loci position along chromosome |

`add` |
additive effect |

`add.sd` |
SD for additive effect |

`dom` |
dominance effect (if present) |

`dom.sd` |
SD for dominance effect |

Brian S. Yandell, yandell@stat.wisc.edu

http://www.stat.wisc.edu/~yandell/qtl/software/Bmapqtl

data( vern ) data( verngeo.bim ) vern.qtl <- bim.effects( verngeo.bim, vern, 2 ) plot.bim.effects( verngeo.bim, vern, 2, qtl = vern.qtl )

[Package *bim* version 1.01-1 Index]