bug fix

irycisBioinfo · Jan 28, 2021 · 0a73f93 · 0a73f93
1 parent 7e6de91
commit 0a73f93
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Showing 4 changed files with 607 additions and 1,984 deletions.
diff --git a/R/accnet_enrichment_analysis.R b/R/accnet_enrichment_analysis.R
@@ -102,7 +102,7 @@ accnet_enrichment_analysis <- function(data,cluster, padj_method = "BY")
     ) %>%
     distinct() %>%
     mutate(
-      OdsRatio =  perClusterFreq / perTotalFreq ,
+      OddsRatio =  perClusterFreq / perTotalFreq ,
       pvalue = phyper(
         ClusterFreq,
         TotalFreq,
@@ -125,7 +125,7 @@ accnet_enrichment_analysis <- function(data,cluster, padj_method = "BY")
     ClusterGenomeSize,
     perTotalFreq,
     TotalFreq,
-    OdsRatio,
+    OddsRatio,
     pvalue,
     padj,
     AccnetGenomeSize,

diff --git a/R/dn_ds.R b/R/dn_ds.R
@@ -121,7 +121,7 @@ dn_ds <- function(mmseq,accnet,min_size =5 ,n_cores,mode = "fast")
 
           name = system(paste0("head -1 ",f,"/",sizes$Family[i]), intern = T)
           system(paste0("sed -i '$ d' ",f,"/",sizes$Family[i]))       ##Remove last line
-          system(paste("head -2 ",f,"/",sizes$Family[i]," > ",f,"/",sizes$Family[i],".ref.fasta",sep = "",collapse = ""))
+          system(paste("head -2 ",f,"/",sizes$Family[i]," > ",f,"/",sizes$Family[i],".ref.fasta",sep = "",collapse = ""))    #### El problema esta por aqui.
           l = system(paste("head -2 ",f,"/",sizes$Family[i],"| tail -1 |wc -m ",sep = "",collapse = ""), intern =T)
           system(paste("grep '>' ",f,"/",sizes$Family[i]," > ",f,"/headers_",sizes$Family[i],sep = "",collapse = ""))
           l = as.numeric(l)*10
@@ -186,6 +186,9 @@ dn_ds <- function(mmseq,accnet,min_size =5 ,n_cores,mode = "fast")
         }
       }
     }
+    else{
+      stop(paste0("Error. Unrecognise mode: ",mode))
+    }
     results <- bind_rows(results,dnds_ratios)
     setwd(mmseq$path)