pool_bs_seq_rep {BPRMeth} | R Documentation

## (DEPRECATED) Read and pool replicates from BS-Seq data

### Description

(DEPRECATED) `pool_bs_seq_rep` reads and pools replicate methylation data from BS-Seq experiments that are either in Encode RRBS or Bismark Cov format. Read the Important section below on when to use this function.

### Usage

    pool_bs_seq_rep(files, file_format = "encode_rrbs", chr_discarded = NULL)

### 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.

### 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

### Important

Unless you want to create a different workflow when processing the BS-Seq data, you should NOT call this function, since this is a helper function. Instead you should call the `preprocess_bs_seq` function.

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`, `preprocess_bs_seq`

### Examples

    # Obtain the path to the file
    bs_file1 <- system.file("extdata", "rrbs.bed", package = "BPRMeth")
    bs_file2 <- system.file("extdata", "rrbs.bed", package = "BPRMeth")

    # Concatenate the files
    bs_files <-  c(bs_file1, bs_file2)
    # Pool the replicates
    pooled_data <- pool_bs_seq_rep(bs_files)

[Package BPRMeth version 1.14.1 Index]