add_expressed_genes: Adding the nearest expressed genes

In eolagbaju/ODER: Optimising the Definition of Expressed Regions

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

eolagbaju/ODER documentation built on Dec. 20, 2021, 5:21 a.m.