createBsseqObject: Helper function to read text files and create a bsseq object.

In boyinggong/MethCP: Differential methylation anlsysis for bisulfite sequencing data

Description

Create a bsseq object when the data for each sample is stored in a separate text file.

Usage

createBsseqObject(
    files, sample_names, 
    chr_col, pos_col, m_col, cov_col, header = TRUE)

Arguments

files	a charactor vector of file names with full path to the file.
sample_names	a charactor vector of sample names. It should have the same length as files vector.
chr_col	name or index of the chromosome column in data files.
pos_col	name or index of the position column in data files.
m_col	name or index of the methylated counts column.
cov_col	name or index of the coverage counts column.
header	a logical value indicating whether the file contains the names of the variables as its first line. dedault TRUE.

Value

a MethCP object that is not segmented.

Examples

library(bsseq)
# The dataset is consist of 6 samples. 3 samples are H2A.Z mutant 
# plants, and 3 samples are controls.
sample_names <- c(
    paste0("control", seq_len(3)), 
    paste0("treatment", seq_len(3))
)

# Get the vector of file path and names 
raw_files <- system.file(
    "extdata", paste0(sample_names, ".txt"), package = "MethCP")

# load the data
bs_object <- createBsseqObject(
    files = raw_files, sample_names = sample_names, 
    chr_col = 'Chr', pos_col = 'Pos', m_col = "M", cov_col = 'Cov')

boyinggong/MethCP documentation built on April 25, 2021, 6:27 p.m.