Entering edit mode
4.7 years ago
MatthewP
★
1.4k
Hello, I need to draw oncoplot with ComplexHeatmap
instead of use oncoplot
function in maftools
for some reason. So I first need to extract plot data from maftools
.
pradMaf <- read.maf("/Work/Mutect2.maf")
# get top 20 genes
geneSummary <- getGeneSummary(pradMaf)[1:20,]
geneList <- geneSummary$Hugo_Symbol
geneSample <- genesToBarcodes(pradMaf, genes = geneList)
I need to know how maftools
classify variant especially Multi_Hit
. It's Multi_Hit
means one gene has multiple types of variant in same sample? Below is variant type stats(same gene), each tibble presents one sample.
# A tibble: 1 x 6
Frame_Shift_Del Frame_Shift_Ins In_Frame_Del Missense_Mutati… Nonsense_Mutati…
<int> <int> <int> <int> <int>
1 4 3 1 46 3
# … with 1 more variable: Splice_Site <int>
# A tibble: 1 x 5
Frame_Shift_Del Frame_Shift_Ins In_Frame_Del Missense_Mutati… Nonsense_Mutati…
<int> <int> <int> <int> <int>
1 3 3 1 42 1
# A tibble: 1 x 4
Frame_Shift_Del Frame_Shift_Ins Missense_Mutation Nonsense_Mutation
<int> <int> <int> <int>
1 6 1 37 4
# A tibble: 1 x 5
Frame_Shift_Del Frame_Shift_Ins Missense_Mutation Nonsense_Mutati… Splice_Site
<int> <int> <int> <int> <int>
1 1 2 36 4 1
If I assign Multi_Hit
for those sample my plot has too many Multi_Hit
compare to plot generate by maftools::oncoplot()
Ok, set
writeMatrix = TRUE
when usingmaftools::oncoplot
function will get oncoplot data, no need to extract byhand. But I will leave question in case some have same problem.