Description Usage Arguments Details Value Examples

View source: R/initiation_points_methods.R

For genes expresing a cryptic transcript, the method allows the identification of cTSS. Five differents methods are available.

1 2 3 4 | ```
initiation_sites(name, bamfiles, types, annotations, introns = NULL,
sf = replicate(length(bamfiles), 1), replicates = 200, percentage = 0.1,
method = c("methodC_gaussian", "methodA", "methodB", "methodC", "methodD"),
paired_end = TRUE, as_fragments = TRUE)
``` |

`name` |
The name of the gene for which to calculate the cryptic initiation site(s). |

`bamfiles` |
a vector of characters indicating the BAM file paths. |

`types` |
a vector of the same length as bamfiles indicating the type of data in each file. Example: WT vs MUT or untreated vs treated". |

`annotations` |
An object of type |

`introns` |
an objet of type |

`sf` |
A vector of the scaling factors to apply to each
sample. Must be the same length as the |

`replicates` |
The number of time to sample the data. Default = 200. |

`percentage` |
Th fraction of data to be removed at each simulation. Default = 0.1. |

`method` |
A character string or a vector specifying the method to use to calculate the cryptic initiations sites. Must be one of "methodC_gaussian" (default), "methodA", "methodB", "methodC" or "methodD". |

`paired_end` |
logical indicating whether the |

`as_fragments` |
logical indicating if paired_end data must paired and merged to form fragments. |

By definition, the observed f value for a gene is the perpendicular distance between the differential cumulative RNA-seq values (type1 - type2) and a diagonal linking the first and last data points. The simulated f max is the maximum f value for a gene after re-sampling the data.

Method A identify a cryptic zone by calculating positions for which the observed f value is in the distribution of simulated f max.

Method B identify a cryptic zone by calculating positions for which the mean simulated f value is in the distribution of simulated f max.

Method C identify a cryptic zone by calculating positions for which the simulated f value is in the distribution of simulated f max.

Method D identify a cryptic zone by calculating the positions for each simulated f max.

Method C gaussian determine the mean and standard deviation of all the positions for which the simulated f value is in the distribution of simulated f max.

A list with the following components:

`methodC_gaussian` |
cTSS mean and sd values using the method C (gaussian) |

`methodA` |
cryptic zones start and end position using the method A |

`methodB` |
cryptic zones start and end position using the method B |

`methodC` |
cryptic zones start and end position using the method C |

`methodD` |
cryptic zones start and end position using the method D |

`gene_information` |
An object of class |

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
data("annotations")
samples <- c("wt_rep1", "wt_rep2", "mut_rep1", "mut_rep2")
bamfiles <- system.file("extdata", paste0(samples, ".bam"),
package = "yCrypticRNAs")
sf <- c(0.069872847, 0.081113079, 0.088520251, 0.069911116)
data(introns)
types = c("wt", "wt", "mut", "mut")
initiation_sites("YER109C", bamfiles, types, annotations,
introns, sf = sf, replicates = 5)
#initiation_sites("YER109C", bamfiles, types, annotations,
# introns, sf = sf, percentage = 0.2, method = "methodA")
``` |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.