add_expressed_genes {ODER} | R Documentation

## Adding the nearest expressed genes

### Description

Updating expressed regions with the expressed gene that is closest to it. After entering the tissue that has been sequenced, the nearest gene and nearest expressed gene will be added to the metadata columns of the annotated ERs.

### Usage

    add_expressed_genes(
      input_file = NULL,
      tissue,
      gtf,
      species = "Homo_sapiens",
      annot_ers,
      type_col_name = "type"
    )

### Arguments

`input_file` | GTEX median expression file, if left as NULL the default file will be used.
`tissue` | Tissue to filter for. See `tissue_options` for options
`gtf` | Either a string containg the path to a .gtf file or a pre-imported gtf using `rtracklayer::import` . Provides gene data to help determine the nearest gene and nearest expressed gene.
`species` | character string containing the species to filter for, Homo sapiens is the default
`annot_ers` | annotated ERs i.e. the product of `annotatERs`, should have an mcols column called "annotation"
`type_col_name` | column name in the gtf file to filter on genes. Default is "type

### Value

Granges with annotated ERs and details of their nearest expressed genes

### Examples

    gtf_url <- paste0(
        "http://ftp.ensembl.org/pub/release-103/gtf/",
        "homo_sapiens/Homo_sapiens.GRCh38.103.chr.gtf.gz"
    )
    gtf_path <- file_cache(gtf_url)
    gtf_gr <- rtracklayer::import(gtf_path)

    ex_opt_ers <- GenomicRanges::GRanges(
        seqnames = S4Vectors::Rle(c("chr21", "chr22"), c(2, 2)),
        ranges = IRanges::IRanges(
            start = c(5116369, 5118691, 5125879, 5128214),
            end = c(5117231, 5118847, 5125988, 5128403)
        )
    )

    ex_opt_ers_w_exp_genes <- add_expressed_genes(
        tissue = "lung", gtf = gtf_gr,
        annot_ers = ex_opt_ers
    )

    ex_opt_ers_w_exp_genes

[Package ODER version 1.0.0 Index]