read_rna_encode_caltech {BPRMeth} | R Documentation

## (DEPRECATED) Read ENCODE Caltech bed formatted RNA-Seq file

### Description

(DEPRECATED) `read_rna_encode_caltech` reads a file containing promoter annotation data together with gene expression levels from RNA-Seq experiments using the `scan` function. The RNA-Seq file should be in ENCODE Caltech `bed` format, e.g. use `gtf2bed` tool if your initial file is in `gtf` format.

### Usage

    read_rna_encode_caltech(file, chr_discarded = NULL, is_GRanges = TRUE)

### Arguments

`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.

### Value

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`

### Author(s)

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

### See Also

`read_chrom_size`, `read_bs_encode_haib`

### Examples

    # Obtain the path to the file and then read it
    rnaseq_file <- system.file("extdata", "rnaseq.bed", package = "BPRMeth")
    rna_data <- read_rna_encode_caltech(rnaseq_file)

[Package BPRMeth version 1.14.1 Index]