I’ve got a sequencing output dataframe. The summary of the variant classification is listed below
3'UTR 5'Flank 5'UTR Frame_Shift_Del 250 13 133 487 Frame_Shift_Ins IGR In_Frame_Del In_Frame_Ins 354 1 651 92 Intron Missense_Mutation Nonsense_Mutation Nonstop_Mutation 8793 6385 517 2 RNA Silent Splice_Site Unknown 278 3062 225 181
I’ve created a oncoplot matrix and replaced the Intron, Silent, 3UTR, 5UTR, 5Flank, RNA, and Unknown with NULL using the following code.
maf_mat <- gsub('Silent;','',maf_mat)
Then I used the complexheatmap oncoprint to create a oncoplot and I got a oncoplot the same as maftools’ one. So I just want to know if oncoplot presents Frame_Shift_Del, Frame_Shift_Ins, In_Frame_Del, In_Frame_Ins, Missense_Mutation, Nonsense_Mutation, and Splice_Site only. And it will ignore the rest variant classification, 3’UTR and Silent for example, by default?
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