Description Usage Arguments Details Value Author(s) References Examples

This is the default test for the differential post-transcriptional RNA modification sites. Differential from all existing tests the compare the absolute amount between two conditions, this test compares whether the percentage of modified molecules are the same.

1 2 3 4 5 | ```
bltest(untreated_ip, untreated_input,
treated_ip, treated_input,
untreated_ip_total, untreated_input_total,
treated_ip_total, treated_input_total,
minimal_count_fdr =10)
``` |

`untreated_ip` |
a vector of integers of n, which is the number of binding sites tested. Each element represents the number of reads fall into a binding site for the IP sample under untreated condition |

`untreated_input` |
a vector of integers of n, which is the number of binding sites tested. Each element represents the number of reads fall into a binding site for the Input control sample under untreated condition |

`treated_ip` |
a vector of integers of n, which is the number of binding sites tested. Each element represents the number of reads fall into a binding site for the IP sample under treated condition |

`treated_input` |
a vector of integers of n, which is the number of binding sites tested. Each element represents the number of reads fall into a binding site for the Input control sample under treated condition |

`untreated_ip_total` |
an integer, total number of reads for the IP sample under untreated condition |

`untreated_input_total` |
an integer, total number of reads for the Input control sample under untreated condition |

`treated_ip_total` |
an integer, total number of reads for the IP sample under treated condition |

`treated_input_total` |
an integer, total number of reads for the Input control sample under treated condition |

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

The comparison of 4 Poisson distributions are firstly collapsed into 2 Binomial distributions, and the function further tests whether the two binomial distributions have the same successful rate with a likelihood ratio 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, from the test.

Lin Zhang, PhD <[email protected]>

Reference coming soon!

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ```
# input reads count of 3 binding sites
untreated_ip = c(10,20,30)
untreated_input = c(20,20,20)
treated_ip = c(30,10,20)
treated_input = c(20,20,20)
# sequencing depths
untreated_ip_total = 10^7
untreated_input_total = 10^7
treated_ip_total = 10^7
treated_input_total = 10^7
# get the result
result = bltest(untreated_ip, untreated_input,
treated_ip, treated_input,
untreated_ip_total, untreated_input_total,
treated_ip_total, treated_input_total)
``` |

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

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