read_bs_bismark_cov: Read Bismark Cov 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_bismark_cov reads a file containing methylation data from BS-Seq experiments using the fread function. The BS-Seq file should be in Bismark Cov format. Read the Important section below on when to use this function.

1	read_bs_bismark_cov(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://rnbeads.mpi-inf.mpg.de/data/RnBeads.pdf

pool_bs_seq_rep, preprocess_bs_seq

## Not run: 
# Download the files and change the working directory to that location
file <- "name_of_bismark_file"
bs_data <- read_bs_bismark_cov(file)

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

## End(Not run)