minor fix

wtsi-hgi · Apr 11, 2024 · 9a3c171 · 9a3c171
1 parent 54f5809
commit 9a3c171
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Showing 2 changed files with 0 additions and 21 deletions.
diff --git a/R/classes.R b/R/classes.R
@@ -308,14 +308,9 @@ create_sampleqc_object <- function(samples) {
     }
 
     samples_meta <- data.frame()
-    samples_info <- vector()
-    samples_exon <- vector()
     list_counts <- list()
     list_lengths <- list()
     for (s in samples) {
-        samples_info <- append(samples_info, s@sample_info)
-        samples_exon <- append(samples_exon, paste0(s@sample_gene, ":Exon", s@sample_exon))
-
         if (nrow(samples_meta) == 0) {
             samples_meta <- data.frame(matrix(NA, 0, length(s@sample_meta)))
             colnames(samples_meta) <- names(s@sample_meta)
@@ -373,8 +368,6 @@ create_sampleqc_object <- function(samples) {
         samples = samples,
         samples_ref = ref_samples,
         samples_meta = samples_meta,
-        samples_info = samples_info,
-        samples_exon = samples_exon,
         counts = list_counts,
         lengths = list_lengths,
         stats = df_stats)
@@ -474,12 +467,7 @@ create_experimentqc_object <- function(samqc_obj,
     }
 
     samples_meta <- data.frame()
-    samples_info <- vector()
-    samples_exon <- vector()
     for (s in samqc_obj@samples) {
-        samples_info <- append(samples_info, s@sample_info)
-        samples_exon <- append(samples_exon, paste0(s@sample_gene, ":Exon", s@sample_exon))
-
         if (nrow(samples_meta) == 0) {
             samples_meta <- data.frame(matrix(NA, 0, length(s@sample_meta)))
             colnames(samples_meta) <- names(s@sample_meta)
@@ -514,8 +502,6 @@ create_experimentqc_object <- function(samqc_obj,
     experimentqc_object <- new("experimentQC",
         samples = samqc_obj@samples,
         samples_meta = samples_meta,
-        samples_info = samples_info,
-        samples_exon = samples_exon,
         coldata = coldata,
         ref_condition = refcond,
         vep_anno = samqc_obj@samples[[1]]@vep_anno,

diff --git a/R/ingest.R b/R/ingest.R
@@ -190,13 +190,6 @@ import_sge_files <- function(dir_path = NULL,
         tmp_obj@per_r1_adaptor <- ifelse(is.na(qc_samplesheet[i, ]$per_r1_adaptor), 0, qc_samplesheet[i, ]$per_r1_adaptor)
         tmp_obj@per_r2_adaptor <- ifelse(is.na(qc_samplesheet[i, ]$per_r2_adaptor), 0, qc_samplesheet[i, ]$per_r2_adaptor)
 
-        tmp_obj@sample_info <- paste(qc_samplesheet[i, ]$targeton_id,
-                                     qc_samplesheet[i, ]$condition,
-                                     qc_samplesheet[i, ]$replicate, sep = "_")
-        tmp_obj@sample_gene <- tmp_obj@vep_anno$symbol[1]
-        tmp_obj@sample_transcript <- tmp_obj@vep_anno$feature[1]
-        tmp_obj@sample_exon <- tmp_obj@vep_anno$exon[1]
-
         tmp_obj@sample_meta["sample_name"] <- tmp_obj@sample
         tmp_obj@sample_meta["sample_info"] <- paste(qc_samplesheet[i, ]$targeton_id,
                                                     qc_samplesheet[i, ]$condition,