pool_bs_seq_rep: Read and pool replicates from BS-Seq data
In andreaskapou/BPRMeth-devel: Model higher-order methylation profiles

Description Usage Arguments Value Important Author(s) See Also Examples

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.

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

`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.

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

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

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

read_bs_bismark_cov, read_bs_encode_haib, preprocess_bs_seq

# 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)