preprocess_bs_seq {BPRMeth} | R Documentation

## (DEPRECATED) Pre-process BS-Seq data in any given format

### Description

(DEPRECATED) `preprocess_bs_seq` is a general function for reading and preprocessing BS-Seq data. If a vector of files is given, these are considered as replicates and are pooled together. Finally, noisy reads are discarded.

### Usage

    preprocess_bs_seq(
      files,
      file_format = "encode_rrbs",
      chr_discarded = NULL,
      min_bs_cov = 4,
      max_bs_cov = 1000
    )

### Arguments

`files` | A vector of filenames containing replicate experiments. This can also be just a single replicate.
`file_format` | A string denoting the file format that the BS-Seq data are stored. Current version allows "`encode_rrbs`" or "`bismark_cov`" formats.
`chr_discarded` | A vector with chromosome names to be discarded.
`min_bs_cov` | The minimum number of reads mapping to each CpG site. CpGs with less reads will be considered as noise and will be discarded.
`max_bs_cov` | The maximum number of reads mapping to each CpG site. CpGs with more reads will be considered as noise and will be discarded.

### Value

A `GRanges` object. The GRanges object contains two additional metadata columns:

- `total_reads`: total reads mapped to each genomic location.

- `meth_reads`: methylated reads mapped to each genomic location.

These columns can be accessed as follows: `granges_object$total_reads`

### Additional Info

Information about the file formats can be found in the following links:

Encode RRBS format: http://rohsdb.cmb.usc.edu/GBshape/cgi-bin/hgTables?db= hg19&hgta_group=regulation&hgta_track=wgEncodeHaibMethylRrbs&hgta_table= wgEncodeHaibMethylRrbsBcbreast0203015BiochainSitesRep2&hgta_doSchema= describe+table+schema

Bismark Cov format: http://rnbeads.mpi-inf.mpg.de/data/RnBeads.pdf

### Author(s)

C.A.Kapourani C.A.Kapourani@ed.ac.uk

### See Also

`read_bs_encode_haib` `pool_bs_seq_rep`

### Examples

    # Obtain the path to the files
    bs_file <- system.file("extdata", "rrbs.bed", package = "BPRMeth")
    bs_data <- preprocess_bs_seq(bs_file, file_format = "encode_rrbs")

[Package BPRMeth version 1.16.0 Index]