Description Usage Arguments Value Author(s) See Also Examples
read_annot_beatson
reads a file containing gene annotation data from
Beatson, using the scan
function.
1 | read_annot_beatson(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:
ensembl_id
: Ensembl IDs of each gene promoter.
gene_name
: Gene name.
These columns can be accessed as follows:
granges_object$ensembl_id
C.A.Kapourani C.A.Kapourani@ed.ac.uk
read_chrom_size
, read_bs_encode_haib
1 2 3 | # Get the location of the annotated Beatson file
annot_beatson_file <- system.file("extdata", "annot_beatson.bed", package = "processHTS")
annot_beatson_data <- read_annot_beatson(file=annot_beatson_file, is_GRanges=TRUE)
|
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