preparingData: preparingData for the miCILP2 data

In ZarnackGroup/m6Aboost: m6Aboost

preparingData for the miCILP2 data

Description

A function for calculating the relative signal strength and extract the features for running the m6Aboost.

Usage

preparingData(object, annotation, colname_reads = "", colname_C2T = "")

Arguments

object	A GRanges object which should contain all single- nucleotide peaks from the miCLIP2 experiment.
annotation	A path to the annotation file. The format of the annotation file should be a gff3 file and downloaded from https://www.gencodegenes.org/
colname_reads	The name of the metadata column which contains the mean value of the truncation reads number without C to T transition reads.
colname_C2T	The name of the meta data column which contains the mean value of C to T transition read counts.

Value

A GRanges object with all information that is required for running the m6Aboost model.

Author(s)

You Zhou

Examples

    testpath <- system.file("extdata", package = "m6Aboost")
    test_gff3 <- file.path(testpath, "test_annotation.gff3")
    test <- readRDS(file.path(testpath, "test.rds"))
    test<- preparingData(test, test_gff3, colname_reads="WTmean",
        colname_C2T="CtoTmean")

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