Description Usage Arguments Details Value References Examples

c-test is used to compare two Poisson means, for peak calling or binding sites identification in exomePeak R-package

1 | ```
ctest(IP, INPUT, TOTAL_IP, TOTAL_INPUT, FOLD = 1, minimal_counts_in_fdr = 10)
``` |

`IP` |
a vector of integers, each elemetnt represents the number of reads from a binding site in the IP sample |

`INPUT` |
a vector of integers, each elements represents the number of reads from a binding site in the Input control sample |

`TOTAL_IP` |
an integer, which represents the total number of reads in IP sample |

`TOTAL_INPUT` |
an integer, which represents the total number of reads in Input control sample |

`FOLD` |
a decimal number, which indicates the ration of Possion mean to be tested, default: 1. Use a larger number for detection of highly enriched binding sites. |

`minimal_counts_in_fdr` |
an integer threshold, only the loci with reads more than this number are subjected for fdr calculation. default: 10 |

c-test is used to compare two Poisson means, for peak calling or binding sites identification in exomePeak R-package. The comparison of two Possion distributions is converted into a binomial distribution based test. The number of reads at the same locus for the aligned reads are counted by other packages, such as Rsamtools or HTseq-count.

The function returns a list of length 3, which contains the log(p-value), log(fdr) and log(fold change), respectively.

Przyborowski, J. and Wilenski, H. (1940) Homogeneity of results in testing samples from Poisson series: with an application to testing clover seed for dodder. Biometrika, 31, 313-323

1 |

exomePeak documentation built on Nov. 1, 2018, 2:26 a.m.

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