read_anno {BPRMeth} | R Documentation

## Read annotation file

### Description

`read_anno` reads a file containing annotation data, which will be used to select genomic regions of interest for downstream analysis. The annotation file format is the following: "chromosome", "start", "end", "strand", "id", "name" (optional). Read the Important section below for more details.

### Usage

    read_anno(
      file,
      chrom_size_file = NULL,
      chr_discarded = NULL,
      is_centre = FALSE,
      is_window = TRUE,
      upstream = -5000,
      downstream = 5000,
      is_anno_region = TRUE,
      delimiter = "\t"
    )

### Arguments

`file` | File name.
`chrom_size_file` | Optional file name to read genome chromosome sizes.
`chr_discarded` | Optional vector with chromosomes to be discarded.
`is_centre` | Logical, whether 'start' and 'end' locations are pre-centred. If TRUE, the mean of the locations will be chosen as centre. If FALSE, the 'start' will be chosen as the center; e.g. for genes the 'start' denotes the TSS and we use this as centre to obtain K-bp upstream and downstream of TSS.
`is_window` | Whether to consider a predefined window region around centre. If TRUE, then 'upstream' and 'downstream' parameters are used, otherwise we consider the whole region from start to end location.
`upstream` | Integer defining the length of bp upstream of 'centre' for creating the genomic region. If is_window = FALSE, this parameter is ignored.
`downstream` | Integer defining the length of bp downstream of 'centre' for creating the genomic region. If is_window = FALSE, this parameter is ignored.
`is_anno_region` | Logical, whether or not to create genomic region. It should be set to TRUE, if you want to use the object as input to `create_region_object` function.
`delimiter` | Delimiter format the columns are splitted. Default is tab.

### Value

A `GRanges` object.

The GRanges object contains two or three additional metadata columns:

- `id`: Feature ID, e.g. Ensembl IDs for each gene.

- `centre`: The central (middle) location of the genomic region. This is required when transforming 'methylation regions' in the (-1, 1) interval, the 'centre' would be at 0.

- `name` (Optional) the feature name.

These columns can be accessed as follows: `granges_obj$id`

### Important

- When having strand information, and we are in the antisense strand ("-"), the 'start' is automatically switched with the 'end' location.

- By default columns are considered in tab delimited format.

- The "name" feature is optional.

- When there is no "strand" info, this can be set to "*".

### Author(s)

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

### See Also

`read_met`, `create_anno_region`, `create_region_object`

### Examples

    # Obtain the path to files
    file <- system.file("extdata", "dummy_anno.bed", package = "BPRMeth")
    anno_dt <- read_anno(file, chr_discarded = c("X"))

    # Extract feature id
    anno_ids <- anno_dt$id

[Package BPRMeth version 1.16.0 Index]