read_encode_cgi: Read file containing CpG island locations
In andreaskapou/BPRMeth-devel: Model higher-order methylation profiles

Description Usage Arguments Value Author(s) See Also Examples

read_encode_cgi reads a file containing CpG island (CGI) locations in the human genome using the fread function.

1	read_encode_cgi(file, is_GRanges = TRUE)

`file`	The name of the file to read data values from.
`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 one additional metadata column:

cgi_id: Unique ID of the CpG Island.

This column can be accessed as follows: granges_object$id

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

read_rna_encode_caltech, read_bs_encode_haib

## Not run: 
# Download the file and change the working directory to that location
file <- "name_of_CGI_file")
cgi_data <- read_encode_cgi(file)

# Extract the CGI ID
cgi_id <- cgi_data$id

## End(Not run)