Description Usage Arguments Value Author(s) Examples

Compute the number of aligned reads overlapping the specified peak intervals for the whole genome.

1 |

`chipdat` |
A list of the starting positions of the ChIP sample aligned reads for each chromosome. The sign of each coordinate represents its strand direction, with a positive numbers on the 5' strand and a negative numbers on the 3' strand. |

`inputdat` |
A list of the starting positions of the input sample aligned reads for each chromosome. The sign of each coordinate represents its strand direction, with a positive numbers on the 5' strand and a negative numbers on the 3' strand. |

`peakpos` |
A list containing the genome coordinates for each peak interval on each chromosome. Each list component is a 2-column matrix containing the left and right boundary of the peak intervals on one chromosome. |

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

`unique` |
A logical value for whether only reads mapping to unique nucleotide positions are counted. |

A list of the numbers of reads that overlap the corresponding peak intervals.

Chandler Zuo zuo@stat.wisc.edu

1 2 3 4 | ```
data( peakpos )
data( tagdat_input )
data( tagdat_chip )
peakcount( tagdat_chip, tagdat_input, peakpos, fragL = 100 )
``` |

CSSP documentation built on Nov. 8, 2020, 8:26 p.m.

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