update

NAMESPACE

@@ -4,6 +4,7 @@ export(BMplotPCA)
 export(DESeq2_module)
 export(biomaRt_anno_orth)
 export(brucemoran_rnaseq_kallisto_parser)
+export(dupradar_run)
 export(edgeR_module)
 export(fgsea_plot)
 export(fgsea_ssgsea_msviper)
@@ -20,6 +21,7 @@ export(make_aracne_inputs)
 export(master_parse_join)
 export(msigdb_pathways_to_list)
 export(nf_core_rnaseq_featco_parser)
+export(nf_core_rnaseq_star_salmon_parser)
 export(obs_raw_widen)
 export(parse_aracne)
 export(per_contrast_fgsea_de)

R/dupradar.R

@@ -18,17 +18,18 @@ dupradar_run <- function(gtf, paired, stranded = '0', threads) {
 
   for (x in 1:length(in_bams)){
 
-  dup_out <- lapply(seq_along(in_bams), function(x){
-    dupo <- dupRadar::analyzeDuprates(in_bams[x], gtf, stranded, paired, threads)
-    pdf(paste0("dupradar/", in_bams[[x]], ".duprate_exp_densplot.pdf"))
-      dupRadar::duprateExpDensPlot(DupMat = dupo)
-    dev.off()
+    dup_out <- lapply(seq_along(in_bams), function(x){
+      dupo <- dupRadar::analyzeDuprates(in_bams[x], gtf, stranded, paired, threads)
+      pdf(paste0("dupradar/", in_bams[[x]], ".duprate_exp_densplot.pdf"))
+        dupRadar::duprateExpDensPlot(DupMat = dupo)
+      dev.off()
 
-    pdf(paste0("dupradar/", in_bams[[x]], ".duprate_exp_boxplot.pdf"))
-      dupRadar::duprateExpBoxplot(DupMat = dupo)
-    dev.off()
-    return(dupo)
-  })
-  names(dup_out) <- in_bams
-  save(dup_out, file="dupradar/dupradar.analyzeDuprates.RData")
+      pdf(paste0("dupradar/", in_bams[[x]], ".duprate_exp_boxplot.pdf"))
+        dupRadar::duprateExpBoxplot(DupMat = dupo)
+      dev.off()
+      return(dupo)
+    })
+    names(dup_out) <- in_bams
+    save(dup_out, file="dupradar/dupradar.analyzeDuprates.RData")
+  }
 }

R/wrapper_scripts.R

@@ -140,7 +140,7 @@ run_prep_modules_bm <- function(metadata_csv, metadata_design, tag, output_dir =
        file = paste0(outdir, "/", tag, ".full_results.RData"))
 
   ##per contrast DE overlap with pathways, and gene sets in lists
-  pc_fgsea_limma_de_list <- per_contrast_fgsea_de(fgsea_list_limma_rank_fithree, occupancy = 5)
+  pc_fgsea_limma_de_list <- RNAseqon::per_contrast_fgsea_de(fgsea_list_limma_rank_fithree, occupancy = 5)
   names(pc_fgsea_limma_de_list) <- names(fgsea_list_limma_rank_fithree)
 
   ##use these as input to ssGSEA in GSVA
@@ -157,7 +157,7 @@ run_prep_modules_bm <- function(metadata_csv, metadata_design, tag, output_dir =
   metadata_pca <- dplyr::select(.data = metadata_tb, sample, !!metadata_cov)
 
   pc_ssgsea_list <- lapply(names(pc_fgsea_limma_de_list), function(f){
-                      ssgsea_pca_list <- ssgsea_pca(pways = pc_fgsea_limma_de_list[[f]][[2]],
+                      ssgsea_pca_list <- RNAseqon::ssgsea_pca(pways = pc_fgsea_limma_de_list[[f]][[2]],
                                                     log2tpm_mat = agg_log2tpm_ext_mat,
                                                     msigdb_cat = "H",
                                                     output_dir = output_dir,
@@ -169,5 +169,5 @@ run_prep_modules_bm <- function(metadata_csv, metadata_design, tag, output_dir =
   ##aracne inputs
   design_vec <- unlist(lapply(metadata_design, function(f){gsub(" ", "", strsplit(f, "\\+")[[1]])}))
   CONDITION <- rev(design_vec)[1]
-  make_aracne_inputs(tpm_tb, metadata = metadata_tb, meta_group = CONDITION, tag = tag)
+  RNAseqon::make_aracne_inputs(tpm_tb, metadata = metadata_tb, meta_group = CONDITION, tag = tag)
 }