From 32f5e097f8c1ceaf451014ac39ab27356289f817 Mon Sep 17 00:00:00 2001
From: theHumanBorch <ncborch@gmail.com>
Date: Fri, 9 Aug 2024 10:44:17 -0500
Subject: [PATCH] Update getIR.R

change nomenclature for light and heavy BCR chains
---
 R/getIR.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/getIR.R b/R/getIR.R
index 39e1916..9ff844c 100644
--- a/R/getIR.R
+++ b/R/getIR.R
@@ -36,15 +36,15 @@ getIR <- function(input.data,
     rownames(meta) <- meta[,"barcode"]
   }
   if(chains %!in% c("TRA", "TRB", "TRG", "TRD", "Heavy", "Light")) {
-    stop("Please select one of the following chains: 'TRA', 'TRB', 'Heavy', 'Light'")
+    stop("Please select one of the following chains: 'TRA', 'TRB', 'TRG', 'TRD' 'Heavy', 'Light'")
   }
   tmp <- data.frame(barcode = rownames(meta), 
                     str_split(meta[,"CTaa"], "_", simplify = TRUE), 
                     str_split(meta[,"CTgene"], "_", simplify = TRUE))
   if (length(chains) == 1 && chains != "both") {
-    if (chains %in% c("TRA", "TRG", "IGH")) { #here
+    if (chains %in% c("TRA", "TRG", "Heavy")) { #here
       pos <- list(c(2,4))
-    } else if (chains %in% c("TRB", "TRD", "IGL", "IGK")) { #here
+    } else if (chains %in% c("TRB", "TRD", "Light")) { #here
       pos <- list(c(3,5))
     }
   } 
@@ -54,12 +54,12 @@ getIR <- function(input.data,
     sub <- as.data.frame(tmp[,c(1,pos[[i]])])
     
     colnames(sub) <- c("barcode", "cdr3_aa", "genes")
-    if(chains %in% c("TRA", "TRG", "Light")) {
+    if(chains %in% c("TRA", "TRG", "Heavy")) {
       sub$v <- str_split(sub$genes, "[.]", simplify = TRUE)[,1]
       sub$d <- NA
       sub$j <- str_split(sub$genes, "[.]", simplify = TRUE)[,2]
       sub$c <- str_split(sub$genes, "[.]", simplify = TRUE)[,3]
-    } else if (chains %in% c("TRB", "TRD", "Heavy")) {
+    } else if (chains %in% c("TRB", "TRD", "Light")) {
       sub$v <- str_split(sub$genes, "[.]", simplify = TRUE)[,1]
       sub$d <- str_split(sub$genes, "[.]", simplify = TRUE)[,2]
       sub$j <- str_split(sub$genes, "[.]", simplify = TRUE)[,3]