I would use lapply to loop lapply columns and then replace " with gsub .
df1[] <- lapply(df1, gsub, pattern='"', replacement='') df1
and if necessary, the class can be changed using type.convert
df1[] <- lapply(df1, type.convert)
data
df1 <- structure(list(ID = c("\"1", "\"2"), name = c("x", "y"), value1 = c("a,\"b,\"c", "d,\"r\""), value2 = c("x\"", "z\"")), .Names = c("ID", "name", "value1", "value2"), class = "data.frame", row.names = c(NA, -2L))
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