Description Usage Arguments Details Value Author(s) Examples

Using a specified ordering of genes, they are split into multiple bins. In each bin, the signal across is summarized and displayed visually.

1 2 3 4 |

`x` |
A |

`summarize` |
How to summarise the scores for each bin into a single value. |

`ordering` |
A |

`ord.label` |
Character string that describes what type of data the ordering is. e.g. "log2 expression". Used to label relevant plot axis. |

`plot.type` |
Style of plot to draw. |

`n.bins` |
The number of bins to split the features into, before summarisation. |

`cols` |
A vector of colours to use for the bins. In order from the lowest value bin, to the highest value bin. |

`lwd` |
Line width of lines in line plot (either scalar or vector). |

`lty` |
Line type of line in line plot (either scalar or vector). |

`same.scale` |
Whether to keep the scale on all plots be the same. |

`symm.scale` |
Whether the scale on plots is symmetrical around 0. |

`verbose` |
Whether to print details of processing. |

If `plotType = "line"`

, a line is plotted for each bin across the promoter.

If `plotType = "heatmap"`

, a series of bins are plotted as a heatmap. This can be useful to display a larger number of bins.

If `plotType = "terrain"`

, a series of bins are plotted as a 3D-terrain map. This can be useful to display a larger number of bins.

Either a single- or multiple-panel figure.

Mark Robinson

1 2 3 4 5 6 7 8 9 10 11 | ```
data(chr21genes)
data(samplesList) # Loads 'samples.list.subset'.
data(expr) # Loads 'expr.subset'.
fs <- featureScores(samples.list.subset, chr21genes, up = 5000, down = 1000, dist = "base", freq = 1000,
s.width = 500)
fs@scores <- list(tables(fs)[[2]] - tables(fs)[[4]])
names(fs) <- "PC-Norm"
binPlots(fs, ordering = expr.subset, ord.label = "expression", plot.type = "line", n.bins = 4)
binPlots(fs, ordering = expr.subset, ord.label = "expression", plot.type = "heatmap", n.bins = 8)
``` |

Repitools documentation built on May 2, 2018, 2:07 a.m.

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