maftools: Summarize, Analyze and Visualize MAF Files

plotMosdepth

R Documentation

Plot results from mosdepth output for Tumor/Normal pair

Description

Plot results from mosdepth output for Tumor/Normal pair

Usage

plotMosdepth(
  t_bed = NULL,
  n_bed = NULL,
  segment = TRUE,
  sample_name = NULL,
  col = c("#95a5a6", "#7f8c8d")
)

Arguments

`t_bed`	mosdepth output from tumor
`n_bed`	mosdepth output from matched normal
`segment`	Performs CBS segmentation. Default TRUE
`sample_name`	sample name. Default parses from 't_bed'
`col`	Colors. Default c("#95a5a6", "#7f8c8d")

Value

Invisibly returns DNAcopy object if 'segment' is 'TRUE'

References

Pedersen BS, Quinlan AR. Mosdepth: quick coverage calculation for genomes and exomes. Bioinformatics. 2018;34(5):867-868. doi:10.1093/bioinformatics/btx699

PoisonAlien/maftools documentation built on Nov. 10, 2024, 6:01 p.m.