The Gene Anchor That Orders a Gene-Centric Non-Coding Table

Source: R/aggregate_coding_results.R

A gene's non-coding masks have different candidate spans (an enhancer can lie far from the gene), so a sort on start separates them. This function gives every gene of a results table one position, its anchor: the bundled gene table's start for a protein-coding gene (the same table GLOWr::define_regions_gene uses), and the smallest start over the gene's rows for a gene not in that table (an ncRNA gene). The scan unit and aggregate_coding_results (through gene_anchor) order rows by (chr, anchor, gene, category).

noncoding_gene_anchor(tbl, genes_info = NULL)

Arguments

tbl

A results table with label (or gene), chr and start columns.

genes_info

A gene table in the layout GLOWr::define_regions_gene accepts, or NULL (the bundled protein-coding table).

Value

A data.frame with one row per (gene, chr): gene, chr, anchor (integer position) and family ("protein_coding" or "other").

Examples

if (FALSE) { # \dontrun{
tbl <- read.csv("runs/myrun/outputs/results-glow/glow_noncoding_chr22.csv")
anchor <- noncoding_gene_anchor(tbl)
} # }