filter_sym: filter a symbol from a table meeting dn8 naming conditions,...

In vjcitn/tnt4dn8: TnT applications with GWAS in dn8 format

filter a symbol from a table meeting dn8 naming conditions, note, hg38 coordinates are expected and not lifted over

Description

filter a symbol from a table meeting dn8 naming conditions, note, hg38 coordinates are expected and not lifted over

Usage

filter_sym(.data, sym, radius = 0)

Arguments

.data	a tbl
sym	a character(1) gene symbol
radius	numeric(1) include 'radius' bp upstream and downstream of gene body limits

Note

if 'pos_b38' is found in the dn8 table, gene addresses from EnsDb.Hsapiens.v79 are used to get gene addresses in hg38 coordinates.

Examples

if (interactive()) {
 data(gtex_b38_lung_chr20_exc)
 chk =  gtex_b38_lung_chr20_exc |> filter_sym("ANGPT4", radius=5e5) |> as.data.frame()
 print(names(chk))
 print(dim(chk))
 print(summary(-log10(chk$p)))
 chk2 = gtex_b38_lung_chr20_exc |> filter_sym("FAM110A", radius=1e6) |> as.data.frame()
 print(dim(chk2))
 print(summary(-log10(chk2$p)))
}

vjcitn/tnt4dn8 documentation built on Sept. 10, 2022, 11:17 a.m.