Description Usage Arguments Value Author(s) Examples

Compute the number of reads overlapping the specified positions for the whole genome.

1 |

`chipdat` |
A list of the starting coordinates for aligned reads for all chromosomes, with positive numbers representing the 5' strand and negative numbers representing the 3' strand. |

`inputdat` |
A list of the starting coordinates for aligned reads for the input sample for all chromosomes, with positive numbers representing the 5' strand and negative numbers representing the 3' strand. |

`bindpos` |
A list of genome coordinates for each chromosome whose numbers of covering tags are computed. |

`fragL` |
A numeric value for the fragment length of the aligned reads. Default: 200. |

`whs` |
A numeric value for the half window size around the binding position. All tags overlapping this region are counted. Default: 250. |

A list of the number of overlapping tags for all position. Each list is a data.frame corresponding to a single chromosome, containing:

chip | The number of ChIP sample reads overlapping each position. |

input | The number of input sample reads overlapping each position. |

Chandler Zuo zuo@stat.wisc.edu

1 2 3 4 | ```
data( tagdat_input )
data( tagdat_chip )
data( bindpos )
bindcount( tagdat_chip, tagdat_input, bindpos, fragL = 100, whs = 300 )
``` |

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