makegrreadsfrombam: Get reads count from bam files of MeRIP-Seq data.

In NWPU-903PR/Funm6AViewer: Visualization of single base differential m6A methylation sites and functional DmM genes

Description

This function will read the bam files to GRanges and save them with their condition id as RData.

Usage

makegrreadsfrombam(IP_bams,
                   Input_bams,
                   condition,
                   minimal_alignment_MAPQ = 30,
                   fragment_length = 100,
                   txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
                   savepath = NA)

Arguments

IP_bams	A vector of characters denote the file path of IP samples in bam formate
Input_bams	A vector of characters denote the file path of input samples in bam formate, should be paired with the IP samples
condition	A vector of characters denote the condition of IP and Input samples. Should be the same length as the ip_bams and the values should be "untreated" or "treated".
minimal_alignment_MAPQ	parameter passed to GenomicAlignments to contol the reads quality.
fragment_length	an integer, which specifies the fragment length in the library preparation, default: 100
txdb	The txdb famate genome annotation. You need to input it similar to "TxDb.Hsapiens.UCSC.hg19.knownGene" if use other genomes instead of hg19.
savepath	The file path where to save the result

Details

This function will read the bam files to GRanges and save them with their condition id as RData.

Value

By default, makegrreadsfrombam will output a list containing the reads count of IP/Input bam files under different condition and the id of each files.

Author(s)

Songyao Zhang

References

Funm6AViewer: Visualization of single base differential m6A methylation sites and functional DmM genes.

NWPU-903PR/Funm6AViewer documentation built on April 25, 2021, 4:26 p.m.