peakcall: Peak calling
In Winnie09/SCATE: SCATE: Single-cell ATAC-seq Signal Extraction and Enhancement

View source: R/peakcall.R

peakcall

R Documentation

Peak calling

Description

Peak calling function

Usage

peakcall(res, flank = 1, fdrcut = 1e-05)

Arguments

`res`	Result matrix returned by SCATE
`flank`	Numeric variable of the number of flanking bins for each bin. For each bin, an averaged signal of itself and the flanking bins will be calculated and compared to a background distribution.
`fdrcut`	Numeric variable of FDR cutoff. Bins passing the FDR cutoff will be peaks.

Details

This function performs peak calling for signal generated by SCATE

Value

A list with length equal to the number of clusters. Each element is a data frame with five columns: chromosome name, starting location, ending location, FDR and signal. The data frame is ordered by FDR then by signal.

Author(s)

Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji* <whou10@jhu.edu>

Examples

gr <- GRanges(seqnames="chr1",IRanges(start=seq_len(100)+1e6,end=seq_len(100)+1e6))
scateout <- SCATE(gr,clunum=156,genome='mm10')[seq_len(1000000),,drop=FALSE]
peakcall(scateout)

Winnie09/SCATE documentation built on May 10, 2023, 8:10 a.m.