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selkamand / sigstash

Easily load published mutational signatures into R
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sigstash sigminer to cosmic indel conversion should turn '_' To ':' not the other way around #29

Closed selkamand closed 3 months ago

selkamand commented 3 months ago

cosmic style indels: 

cosmic_style_indels <- c("1:Del:C:0", "1:Del:C:1", "1:Del:C:2", "1:Del:C:3", "1:Del:C:4", 
"1:Del:C:5", "1:Del:T:0", "1:Del:T:1", "1:Del:T:2", "1:Del:T:3", 
"1:Del:T:4", "1:Del:T:5", "1:Ins:C:0", "1:Ins:C:1", "1:Ins:C:2", 
"1:Ins:C:3", "1:Ins:C:4", "1:Ins:C:5", "1:Ins:T:0", "1:Ins:T:1", 
"1:Ins:T:2", "1:Ins:T:3", "1:Ins:T:4", "1:Ins:T:5", "2:Del:R:0", 
"2:Del:R:1", "2:Del:R:2", "2:Del:R:3", "2:Del:R:4", "2:Del:R:5", 
"3:Del:R:0", "3:Del:R:1", "3:Del:R:2", "3:Del:R:3", "3:Del:R:4", 
"3:Del:R:5", "4:Del:R:0", "4:Del:R:1", "4:Del:R:2", "4:Del:R:3", 
"4:Del:R:4", "4:Del:R:5", "5:Del:R:0", "5:Del:R:1", "5:Del:R:2", 
"5:Del:R:3", "5:Del:R:4", "5:Del:R:5", "2:Ins:R:0", "2:Ins:R:1", 
"2:Ins:R:2", "2:Ins:R:3", "2:Ins:R:4", "2:Ins:R:5", "3:Ins:R:0", 
"3:Ins:R:1", "3:Ins:R:2", "3:Ins:R:3", "3:Ins:R:4", "3:Ins:R:5", 
"4:Ins:R:0", "4:Ins:R:1", "4:Ins:R:2", "4:Ins:R:3", "4:Ins:R:4", 
"4:Ins:R:5", "5:Ins:R:0", "5:Ins:R:1", "5:Ins:R:2", "5:Ins:R:3", 
"5:Ins:R:4", "5:Ins:R:5", "2:Del:M:1", "3:Del:M:1", "3:Del:M:2", 
"4:Del:M:1", "4:Del:M:2", "4:Del:M:3", "5:Del:M:1", "5:Del:M:2", 
"5:Del:M:3", "5:Del:M:4", "5:Del:M:5")

sigminer style

1_Del_C_0, 1_Del_C_1, 1_Del_C_2, 1_Del_C_3, 1_Del_C_4,
  1_Del_C_5, 1_Del_T_0, 1_Del_T_1, 1_Del_T_2, 1_Del_T_3, 1_Del_T_4, 1_Del_T_5,
  1_Ins_C_0, 1_Ins_C_1, 1_Ins_C_2, 1_Ins_C_3, 1_Ins_C_4, 1_Ins_C_5, …, 5_Ins_R_4, and
  5_Ins_R_5.
selkamand commented 3 months ago

Note that cosmic-style SVs actually do require a : to _ conversion. Its only indels that go the other way.