preprocess_bs_seq {BPRMeth} | R Documentation |
(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.
preprocess_bs_seq(files, file_format = "encode_rrbs", chr_discarded = NULL, min_bs_cov = 4, max_bs_cov = 1000)
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. |
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. |
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
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
pool_bs_seq_rep
# 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")