meRatio: Observed m6A methylation ratio.

In ZhenxingGuo0015/TRESS: Toolbox for mRNA epigenetics sequencing analysis

Observed m6A methylation ratio.

Description

This function calculates, for each candidate region, the enrichment of normalized IP read counts versus the sum of normalized IP and input control read counts.

Usage

meRatio(counts, sf)

Arguments

counts	A data matrix containing read counts in each region across sample input1, ip1, input2, ip2, input3, ip3, ...
sf	A numerical vector containing the size factor of each sample, which is used for sequencing depth normalization. The sample order here is the same as that in counts.

Value

ratio

A numerical data matrix containing the methylation ratio of each candidate region across all samples. Here, the number of columns is half of the number of columns in read count matrix.

Examples

data("Basal")
## methylatinon ratio
Ratio = meRatio(
    counts = Basal$Candidates$Counts,
    sf = Basal$Bins$sf
    )
head(Ratio, 3)

ZhenxingGuo0015/TRESS documentation built on April 14, 2023, 4:21 p.m.