pool_bs_seq_rep {BPRMeth} | R Documentation |
(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.
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 " |
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:
Bismark Cov format: http://rnbeads.mpi-inf.mpg.de/data/RnBeads.pdf
C.A.Kapourani C.A.Kapourani@ed.ac.uk
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)