CtoTAssignment: CtoTAssignment for assigning the truncation read counts to...

In ZarnackGroup/m6Aboost: m6Aboost

CtoTAssignment for assigning the truncation read counts to the GRanges object with single nucleotide peaks

Description

An function for assigning the CtoT transition read counts from bigWig.

Usage

CtoTAssignment(object, bw_positive, bw_negative, sampleName = "")

Arguments

object	A GRanges object which should contains all the single nucleotide peaks of miCLIP2 experiment.
bw_positive	A path to the bigWig file of C to T transition read counts at the positive strand that output from the preprocess in the m6Aboost pipeline.
bw_negative	A path to the bigWig file of C to T transition read counts at the negative strand that output from the preprocess in the m6Aboost pipeline.
sampleName	The column name that user would like to use for indicating the name of the sample.

Value

A GRanges object with the truncation read counts.

Author(s)

You Zhou

Examples

if (.Platform$OS.type != "windows") {
    testpath <- system.file("extdata", package = "m6Aboost")
    test <- readRDS(file.path(testpath, "test.rds"))
    ctotBw_p <- file.path(testpath, "C2T_positive.bw")
    ctotBw_n <- file.path(testpath, "C2T_negative.bw")
    test <- CtoTAssignment(test, bw_positive=ctotBw_p, bw_negative=ctotBw_n,
        sampleName = "CtoT_WT1")
}

ZarnackGroup/m6Aboost documentation built on Dec. 8, 2023, 11:26 p.m.