getBaseModificationDf.BSseq: get the information of base modification

In YuLab-SMU/BMplot: BMplot for Base Modification Visulization

get the information of base modification

Description

This function retrieve the information of each base, requiring BSseq object as input. Then organized it to dataframe.

Usage

getBaseModificationDf.BSseq(
  region,
  input,
  BSgenome,
  cover_depth = TRUE,
  base = NULL,
  motif = NULL,
  position_bias = NULL
)

Arguments

region	base modification region in the form of dataframe, having columns of "chr","start" and "end"
input	the input data stored in BSseq objects
BSgenome	genome reference
cover_depth	take the depth of cover into account or not
base	one of A/T/G/C/U
motif	the motif(e.g C:CG/CH, A:GAGG/AGG) of the base modification
position_bias	1-base bias. e.g position_bias = 1("C" in "CHH"), position_bias = 2("A" in "GAGG")

Value

dataframe

YuLab-SMU/BMplot documentation built on June 1, 2025, 4:09 p.m.