getBaseModificationDf-methods: getBaseModificationDf methods generics

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

getBaseModificationDf methods generics

Description

getBaseModificationDf method for BSseq

getBaseModificationDf method for bmData

Usage

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

## S4 method for signature 'ANY,BSseq'
getBaseModificationDf(
  region,
  input,
  BSgenome,
  base = NULL,
  motif = NULL,
  position_bias = NULL,
  cover_depth = TRUE,
  ...
)

## S4 method for signature 'ANY,bmData'
getBaseModificationDf(
  region,
  input,
  BSgenome,
  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 or BSseqExtra objects
BSgenome	genome reference
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")
...	other parameters
cover_depth	take the depth of cover into account or not

Value

dataframe

dataframe

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