diff --git a/bin/QC/array_study_QC_report.Rmd b/bin/QC/array_study_QC_report.Rmd index 29e399c..d6ce064 100644 --- a/bin/QC/array_study_QC_report.Rmd +++ b/bin/QC/array_study_QC_report.Rmd @@ -89,7 +89,7 @@ message("Number of samples in study after quality control: ", sample_metadata[sa Performs principal component analysis (PCA) of gene expression data ```{r pca_res, echo=FALSE} -valid_gene_types = c("lincRNA","protein_coding","IG_C_gene","IG_D_gene","IG_J_gene", +valid_gene_types = c("lincRNA","lncRNA","protein_coding","IG_C_gene","IG_D_gene","IG_J_gene", "IG_V_gene", "TR_C_gene","TR_D_gene","TR_J_gene", "TR_V_gene", "3prime_overlapping_ncrna","known_ncrna", "processed_transcript", "antisense","sense_intronic","sense_overlapping") diff --git a/bin/QC/rnaseq_study_QC_report.Rmd b/bin/QC/rnaseq_study_QC_report.Rmd index 0ac3641..7af996a 100644 --- a/bin/QC/rnaseq_study_QC_report.Rmd +++ b/bin/QC/rnaseq_study_QC_report.Rmd @@ -102,7 +102,7 @@ Performs principal component analysis (PCA) of gene expression data * log2(matrix + 0.1) is applied ```{r pca_res, echo=FALSE} -valid_gene_types = c("lincRNA","protein_coding","IG_C_gene","IG_D_gene","IG_J_gene", +valid_gene_types = c("lincRNA","lncRNA","protein_coding","IG_C_gene","IG_D_gene","IG_J_gene", "IG_V_gene", "TR_C_gene","TR_D_gene","TR_J_gene", "TR_V_gene", "3prime_overlapping_ncrna","known_ncrna", "processed_transcript", "antisense","sense_intronic","sense_overlapping")