Merge pull request #330 from JHYSiu/loadContigs_Immcantation

Update loadContigs.R Immcantation loading
ncborcherding · Mar 7, 2024 · 83ab850 · 83ab850
2 parents 50eb0fa + baf8377
commit 83ab850
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/R/loadContigs.R b/R/loadContigs.R
@@ -55,7 +55,7 @@ loadContigs <- function(input,
 
         if (format %in% c("10X", "WAT3R", "Omniscope")) {
           df <- lapply(contig.files, read.csv) 
-        } else if("json") { 
+        } else if(format %in% c("json")) { 
           df <- lapply(contig.files, function(x) {
             tmp <- as.data.frame(fromJSON(x))
           })
@@ -229,9 +229,9 @@ loadContigs <- function(input,
   for (i in seq_along(df)) {
     df[[i]][df[[i]] == ""] <- NA
     df[[i]] <- as.data.frame(df[[i]])
-    df[[i]] <- df[[i]][,c("sequence_id", "locus", "consensus_count",  "v_call", "d_call", "j_call", "c_gene", "cdr3", "cdr3_aa")]
+    df[[i]] <- df[[i]][,c("sequence_id", "locus", "consensus_count",  "v_call", "d_call", "j_call", "c_call", "cdr3", "cdr3_aa")]
     colnames(df[[i]]) <- c("barcode", "chain", "reads", "v_gene", "d_gene", "j_gene", "c_gene", "cdr3_nt", "cdr3")
-    df[[i]] <- str_split(df[[i]][,"barcode"], "_", simplify = TRUE)[,1]
+    df[[i]]$barcode <- str_split(df[[i]][,"barcode"], "_", simplify = TRUE)[,1]
   }
   return(df)
 }