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.
add_expressed_genes(
input_file = NULL,
tissue,
gtf,
species = "Homo_sapiens",
annot_ers,
type_col_name = "type"
)| input_file | GTEX median expression file, if left as NULL the default file will be used. |
|---|---|
| tissue | Tissue to filter for. See |
| gtf | Either a string containg the path to a .gtf file or a pre-imported
gtf using |
| species | character string containing the species to filter for, Homo sapiens is the default |
| annot_ers | annotated ERs i.e. the product of |
| type_col_name | column name in the gtf file to filter on genes. Default is "type |
Granges with annotated ERs and details of their nearest expressed genes
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
#> GRanges object with 4 ranges and 2 metadata columns:
#> seqnames ranges strand | nearest_gene_v94_name
#> <Rle> <IRanges> <Rle> | <character>
#> [1] chr21 5116369-5117231 * | ENSG00000276612
#> [2] chr21 5118691-5118847 * | ENSG00000276612
#> [3] chr22 5125879-5125988 * | ENSG00000277248
#> [4] chr22 5128214-5128403 * | ENSG00000277248
#> nearest_expressed_gene_v94_name
#> <character>
#> [1] ENSG00000264462
#> [2] ENSG00000264462
#> [3] ENSG00000206195
#> [4] ENSG00000206195
#> -------
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths