yCrypticRNAs (version 0.99.2)

initiation_sites: Cryptic transcription start sites (cTSS)

Description

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

Usage

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)

Arguments

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 annotationsSet containing information on genes.

introns

an objet of type annotationsSet containing the annotations of the intronic regions. Note: The introns must have same name as the gene they are associated with.

sf

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

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 bamfile contains paired_end data.

as_fragments

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

Value

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 annotationsSet containing the information on the gene.

Details

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.

Examples

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")