detection5: Detection of start regions

In Simon-Leonard/APERO: Analysis of Paired-End RNA-seq Output

Detection of start regions

Description

This is the main function of the APERO's first module dedicatied to start region detection, which are defined as regions exhibiting a local enrichment in read starts compared to neighbor regions.

Usage

 detection5(d,wmax,flanks,seuil_net,genome_size)

Arguments

d	data.frame with the following column names : 5end, str, sum_freq. The 5end column has to be the first column of the data.fame. It contains 5' positions of mapped reads. The str column contains corresponding strand. The sum_freq columns contains the number of mapped reads with the corresponding 5' position and strand.
wmax	Maximal size of the window to compute local enrichment. Has to be an odd number and is equal to 2*maximal width+1.
flanks	Size of the neighboring region to compute local enrichment. A vector containing multiple sizes can also be used.
seuil_net	Enrichment threshold to identify start regions
genome_size	Genome size

Value

A start region data.frame described with central position, positionnal uncertainty, strand, and number of starting reads

Author(s)

Simon Leonard

Simon-Leonard/APERO documentation built on June 17, 2022, 10:31 a.m.