From 437ae6de84a6953d031db1ba60e155689ab107ce Mon Sep 17 00:00:00 2001 From: Elias Projahn Date: Sun, 29 Aug 2021 14:02:37 +0200 Subject: [PATCH] Include data on TPE-OLD status of genes --- input.R | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/input.R b/input.R index affa8b7..3c7ac52 100644 --- a/input.R +++ b/input.R @@ -1,6 +1,30 @@ library(data.table) library(rlog) +#' Gene names of genes for verified TPE-OLD genes. +genes_verified_tpe_old <- c( + "C1S", + "DSP", + "ISG15", + "SORBS2", + "TERT" +) + +#' Gene names of genes with a suggested TPE-OLD. +genes_suggested_tpe_old <- c( + "AKAP3", + "ANO2", + "CCND2", + "CD163L1", + "CD9", + "FOXM1", + "GALNT8", + "NDUFA9", + "TEAD4", + "TIGAR", + "TSPAN9" +) + #' Merge genome data from files in `path` into `data.table`s. #' #' The result will be a list with named elements: @@ -8,7 +32,14 @@ library(rlog) #' - `species` will contain metadata on each species. #' - `distances` will contain each species' genes' distances to the telomere. load_input <- function(path) { + # Include data on TPE-OLD status for genes. + genes <- fread(paste(path, "genes.tsv", sep = "/")) + genes[name %chin% genes_verified_tpe_old, verified := TRUE] + genes[name %chin% genes_suggested_tpe_old, suggested := TRUE] + + # Load and combine data on species and gene distances. + original_species <- fread(paste(path, "species.csv", sep = "/")) species <- data.table(