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R/DNA_sequence_cos.R

@@ -1,4 +1,4 @@
-#' Obtain all mutations codons
+ #' Obtain all mutations codons
 #'
 #' This function will load all the CDS from the mutated genes in the input file. Then recovery the 3' and
 #' 5' nucleotide aside of the mutation site.
@@ -7,8 +7,11 @@
 #' @param num The number of patient you want to analyse. Default will go through all the dataset.
 #' @return DNA_seq = CDS sequence for all the genes used, codon_part = codon around mutation.
 #' @export
-DNA_sequence_cos = function(cosmic,num = length(cosmic$GENE_NAME)){
-
+DNA_sequence_cos = function(cosmic,num = length(cosmic$GENE_NAME),random = FALSE){
+  if (random == TRUE){
+    idx = sort(sample(1:length(cosmic$GENE_NAME),num, replace = F))
+    cosmic = cosmic[idx,]
+  }
   genes_mut_names = sapply(strsplit(cosmic$GENE_NAME[1:num],"[\\_]+"), `[`, 1)
   genes_mut_site1 = sapply(strsplit(cosmic$MUTATION_CDS[1:num],"[\\c.]+"), `[`, 2)
   genes_mut_site = as.numeric(str_extract(genes_mut_site1, "[0-9]+"))

R/Signature_algoV2.R

@@ -8,21 +8,21 @@
 #' @return change_nu = the change of nucleotide due to the mutation, mut_to = the codon paste to
 #' the nucleotide after mutation.
 #' @export
-Signature_algoV2 = function(file,num){
+Signature_algoV2 = function(file,num, random = FALSE){
   for(i in 1:length(file)){
     if( i == 1){
       print("Running into file 1")
       data = import_data_cos(file[i])
-      seq = DNA_sequence_cos(data,num)
+      seq = DNA_sequence_cos(data,num,random)
       mut_to = Site_mut_cos(seq)
-      mut_signa = mut_signature_cos(mut_to, data, i)
+      mut_signa = mut_signature_cos(mut_to, i)
       next
     }
     print(c("Running into file", i))
     data = import_data_cos(file[i])
-    seq = DNA_sequence_cos(data,num)
+    seq = DNA_sequence_cos(data,num,random)
     mut_to = Site_mut_cos(seq)
-    mut_signa1 = mut_signature_cos(mut_to, data, i)
+    mut_signa1 = mut_signature_cos(mut_to, i)
     mut_signa = rbind(mut_signa,mut_signa1)
   }
   mut_signa$cancer = as.factor(mut_signa$cancer)