createBsseqObject {MethCP} | R Documentation

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

### 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')

[Package MethCP version 1.8.0 Index]