EDfromBams: To get editing distance from multiple bam files

In jknightlab/AltHapAlignR: AltHapAlignR: Haplotype-specific mapping in RNA-seq

Description

To get editing distance from multiple bam files

Usage

EDfromBams(bamFiles, gtf, output_name = "ed_table.txt", virtualenv = 0,
  r = "VARSL-VARS2,C6orf205-MUC21")

Arguments

bamFiles	bam files <path/to/BAM_file_1> <path/to/BAM_file_2>
gtf	gtf file <path/to/GTF_file>
output_name	output name
virtualenv	path of virtualenv, optional
r	combine redundnat gene names, example, VARSL-VARS2,C6orf205-MUC21, optional

Examples

bamFiles=system.file("extdata", "mapping2*bam", package = "AltHapAlignR")
gtf=system.file("extdata", "gencode.v21.chr_patch_hapl_HLA.annotation.gtf", 
                 package = "AltHapAlignR")
EDfromBams(bamFiles, gtf, output_name="output.txt", virtualenv=0, r="VARSL-VARS2,C6orf205-MUC21")

jknightlab/AltHapAlignR documentation built on Sept. 11, 2019, 9:02 p.m.