NET5: NET5 function used in the first module of the APERO programm...

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

NET5 function used in the first module of the APERO programm dedicated to the identification of 5' end RNAs.

Description

Compute the local enrichment value as described in the paper

Usage

NET5(test,window_size,flanks_size,genome_size)

Arguments

test	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
window_size	Size of the window to compute local enrichment. Has to be an odd number and is equal to 2w+1 corresponding to the local enrichment formula described in the paper.
flanks_size	Size of the neighboring region to compute local enrichment. Corresponds to f in the local enrichment formula described in the paper.
genome_size	Genome size

Value

The test data.frame with an additional column containing the local enrichment value.

Author(s)

Simon Leonard

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