Description Usage Arguments Details Author(s) See Also Examples

View source: R/manhattanPlot.R

Generates a manhattan plot of the results of a genome wide association test.

1 2 3 |

`p` |
A vector of p-values. |

`chromosome` |
A vector containing the chromosome for each SNP. |

`ylim` |
The limits of the y axis. If NULL, the y axis is |

`trunc.lines` |
Logical value indicating whether to show truncation lines. |

`signif` |
Genome-wide significance level for plotting horizontal
line. If |

`thinThreshold` |
if not |

`pointsPerBin` |
number of points to plot in each bin if |

`col` |
vector containing colors of points; defaults to coloring by chromosome using the colorbrewer Dark2 palette with 8 colors |

`...` |
Other parameters to be passed directly to |

Plots -log10(p) versus chromosome. Point size is scaled so that smaller p values have larger points.

`p`

must have the same length as `chromosome`

and is
assumed to be in order of position on each chromosome. Values within
each chromosome are evenly spaced along the X axis.

Plot limits are determined as follows: if `ylim`

is provided, any
points with `-log10(p) > ylim[2]`

are plotted as triangles at the
maximum y value of the plot. A line will be drawn to indicate
trunctation (if `trunc.lines == TRUE`

, the default). If
`ylim == NULL`

, the maximum y value is defined as
`log10(length(p)) + 4)`

.

If requested with `thinThreshold`

, points with `-log10(pval) < thinThreshold`

are thinned before plotting. All points with `-log10(pval) >= thinThreshold`

are displayed. P-values with `-log10(pval) < thinThreshold`

are sampled such that `pointsPerBin`

points are randomly selected from 10 bins with uniform spacing in `-log10(pval)`

space.

Cathy Laurie, Adrienne Stilp

1 2 3 4 5 |

```
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
```

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