read_rna_beatson: Read Beatson bed formatted RNA-Seq file
In andreaskapou/processHTS: Process HTS Files and Data

Description Usage Arguments Value Author(s) See Also Examples

read_rna_beatson reads a file containing promoter annotation data together with gene expression levels from RNA-Seq experiments using the fread function.

1	read_rna_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 three additional metadata columns:

ensembl_id: Ensembl IDs of each gene promoter.
gene_name: Gene name.
gene_fpkm: Expression level in FPKM.

These columns can be accessed as follows: granges_object$ensembl_id

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

read_annot_beatson, read_bs_bismark_cov

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# Get the location of the RNA-Seq file
rna_beatson_file <- system.file("extdata", "rna_beatson.bed", package = "processHTS")
rna_beatson_data <- read_rna_beatson(file=rna_beatson_file, chr_discarded = "chrX", is_GRanges=TRUE)