CallPeaks.multiRep: m6A peak calling with multiple replicates.

In haowulab/TRESS: Toolbox for mRNA epigenetics sequencing analysis

m6A peak calling with multiple replicates.

Description

This function identifies and ranks significant m6A peaks, given candidate regions obtained from multiple paired of input \& IP replicates.

Usage

CallPeaks.multiRep(Candidates, mu.cutoff,
                   WhichThreshold = "fdr_lfc",
                   pval.cutoff = 1e-5,
                   fdr.cutoff = 0.05,
                   lfc.cutoff = 0.7)

Arguments

Candidates	A list containing: genomic coordinates of each candidate region, read counts and log fold change between IP and input in each candidate region. It also contains the size factor of each sample.
mu.cutoff	A constant specifying the background methylation levels. This is estimated automatically based on the first step of peak calling.
WhichThreshold	A character specifying a threshold for significant peaks. There are three options: "pval" (only use p-values), "fdr" (only use FDR), "lfc" (only use log fold change), "pval_lfc" (use both p-values and log fold changes) and "fdr_lfc" (use FDR and log fold changes). Default is "fdr_lfc".
pval.cutoff	A constant indicating the cutoff for p-value. Default is 1e-05.
fdr.cutoff	A constant indicating the cutoff for FDR. Default is 0.05.
lfc.cutoff	A constant indicating the cutoff for log fold change. Default is 0.7 for fold change of 2.

Details

This function first calls CallPeaks.paramEsti to conduct parameter estimation and hypothesis testing for all candidate m6A regions. Then it filters and ranks candidate regions using respective criteria to obtain a list of significant m6A peaks.

Value

The output is a dataframe whose columns are:

chr	Chromosome number of each peak.
start	The start of genomic position of each peak.
end	The end of genomic position of each peak.
strand	The strand of each peak.
summit	The summit of each peak.
lg.fc	Log fold change between normalized IP and normalized input read counts.
mu	Methylation level of each peak if there are more than one replicates.
mu.var	Estimated variance of methylation level for each peak, when there are more than one replicates.
stats	Wald test statistics of each peak, when there are more than one replicate.
shrkPhi	Shrinkage estimation of mehtylation dispersion for each peak, when there are more than one replicates.
shrkTheta	Shrinkage estimation for scale parameter theta in the gamma distribution, when there are more than one replicates.
pvals	P-value calculated based on the Wald-test.
p.adj	Adjusted p-values using Benjamini-Hochberg procedure.
rSocre	A score used to rank each peak. The higher the score, the higher the rank would be.

Note, there are additional columns with name "*.bam". These columns contain the read counts from respective samples.

Examples

### A toy example
data("Basal")
CallPeaks.multiRep(
    Candidates = Basal$Candidates,
    mu.cutoff = 0.5
    )

haowulab/TRESS documentation built on Aug. 27, 2022, 7:11 p.m.