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Include data on TPE-OLD status of genes

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This commit is contained in:
Elias Projahn 2021-08-29 14:02:37 +02:00
parent 42d8da7e77
commit 437ae6de84
1 changed files with 31 additions and 0 deletions
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31
input.R
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@ -1,6 +1,30 @@
library(data.table) library(data.table)
library(rlog) 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. #' Merge genome data from files in `path` into `data.table`s.
#' #'
#' The result will be a list with named elements: #' The result will be a list with named elements:
@ -8,7 +32,14 @@ library(rlog)
#' - `species` will contain metadata on each species. #' - `species` will contain metadata on each species.
#' - `distances` will contain each species' genes' distances to the telomere. #' - `distances` will contain each species' genes' distances to the telomere.
load_input <- function(path) { load_input <- function(path) {
# Include data on TPE-OLD status for genes.
genes <- fread(paste(path, "genes.tsv", sep = "/")) 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 = "/")) original_species <- fread(paste(path, "species.csv", sep = "/"))
species <- data.table( species <- data.table(