read_bs_encode_haib: Read ENCODE HAIB bed formatted BS-Seq file
In andreaskapou/BPRMeth-devel: Model higher-order methylation profiles

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

read_bs_encode_haib reads a file containing methylation data from BS-Seq experiments using the scan function. The BS-Seq file should be in ENCODE HAIB bed format. Read the Important section below on when to use this function.

1	read_bs_encode_haib(file, chr_discarded = NULL, is_GRanges = TRUE)

`file`	The name of the file to read data values from.
`chr_discarded`	A vector with chromosome names to be discarded.
`is_GRanges`	Logical: if TRUE a GRanges object is returned, otherwise a data.frame object is returned.

A GRanges object if is_GRanges is TRUE, otherwise a data.table 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.

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

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

pool_bs_seq_rep, preprocess_bs_seq

# Obtain the path to the file and then read it
bs_file <- system.file("extdata", "rrbs.bed", package = "BPRMeth")
bs_data <- read_bs_encode_haib(bs_file)

# Extract the total reads and methylated reads
total_reads <- bs_data$total_reads
meth_reads <- bs_data$meth_reads