Convert a dataframe to presence absence matrix

by

One possibility:

library(reshape2)
df2 <- melt(df, id.var = "V1")
with(df2, table(V1, value))

#         value
# V1      A B C D E F
#   File1 1 1 1 0 0 0
#   File2 1 1 0 1 0 0
#   File3 0 0 0 0 1 1

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