read_bedgraphs {methrix} | R Documentation

## Versatile BedGraph reader.

### Description

Versatile BedGraph reader.

### Usage

    read_bedgraphs(
      files = NULL,
      pipeline = NULL,
      zero_based = TRUE,
      stranded = FALSE,
      collapse_strands = FALSE,
      ref_cpgs = NULL,
      ref_build = NULL,
      contigs = NULL,
      vect = FALSE,
      vect_batch_size = NULL,
      coldata = NULL,
      chr_idx = NULL,
      start_idx = NULL,
      end_idx = NULL,
      beta_idx = NULL,
      M_idx = NULL,
      U_idx = NULL,
      strand_idx = NULL,
      cov_idx = NULL,
      synced_coordinates = FALSE,
      n_threads = 1,
      h5 = FALSE,
      h5_dir = NULL,
      h5temp = NULL,
      verbose = TRUE
    )

### Arguments

`files` | bedgraph files.
`pipeline` | Default NULL. Currently supports "Bismark_cov", "MethylDackel", "MethylcTools", "BisSNP", "BSseeker2_CGmap" If not known use idx arguments for manual column assignments.
`zero_based` | Are bedgraph regions zero based ? Default TRUE
`stranded` | Default FALSE
`collapse_strands` | If TRUE collapses CpGs on different crick strand into watson. Deafult FALSE
`ref_cpgs` | BSgenome object, or name of the installed BSgenome package, or an output from `extract_CPGs`. Example: BSgenome.Hsapiens.UCSC.hg19
`ref_build` | reference genome for bedgraphs. Default NULL. Only used for additional details. Doesnt affect in any way.
`contigs` | contigs to restrict genomic CpGs to. Default all autosomes and allosomes - ignoring extra contigs.
`vect` | To use vectorized code. Default FALSE. Set to TRUE if you don't have large number of BedGraph files.
`vect_batch_size` | Default NULL. Process samples in batches. Applicable only when vect = TRUE
`coldata` | An optional DataFrame describing the samples. Row names, if present, become the column names of the matrix. If NULL, then a DataFrame will be created with basename of files used as the row names.
`chr_idx` | column index for chromosome in bedgraph files
`start_idx` | column index for start position in bedgraph files
`end_idx` | column index for end position in bedgraph files
`beta_idx` | column index for beta values in bedgraph files
`M_idx` | column index for read counts supporting Methylation in bedgraph files
`U_idx` | column index for read counts supporting Un-methylation in bedgraph files
`strand_idx` | column index for strand information in bedgraph files
`cov_idx` | column index for total-coverage in bedgraph files
`synced_coordinates` | Are the start and end coordinates of a stranded bedgraph are synchronized between + and - strands? Possible values: FALSE (default), TRUE if the start coordinates are the start coordinates of the C on the plus strand.
`n_threads` | number of threads to use. Default 1. Be-careful - there is a linear increase in memory usage with number of threads. This option is does not work with Windows OS.
`h5` | Should the coverage and methylation matrices be stored as 'HDF5Array'
`h5_dir` | directory to store H5 based object
`h5temp` | temporary directory to store hdf5
`verbose` | Be little chatty ? Default TRUE.

### Details

Reads BedGraph files and generates methylation and coverage matrices. Optionally arrays can be serialized as on-disk HDFS5 arrays.

### Value

An object of class `methrix`

### Examples

    ## Not run:
    bdg_files = list.files(path = system.file('extdata', package = 'methrix'),
    pattern = '*\\.bedGraph\\.gz$', full.names = TRUE)
    hg19_cpgs = methrix::extract_CPGs(ref_genome = 'BSgenome.Hsapiens.UCSC.hg19')
    meth = methrix::read_bedgraphs( files = bdg_files, ref_cpgs = hg19_cpgs,
    chr_idx = 1, start_idx = 2, M_idx = 3, U_idx = 4,
    stranded = FALSE, zero_based = FALSE, collapse_strands = FALSE)

    ## End(Not run)

[Package methrix version 1.4.07 Index]