match

match.R

# Some example data
# Data frame with an id column
data1 <- data.frame(ids = c("A", "B", "C"), value = 1:3)

# matrix with rownames for ids
data2 <- matrix(1:20, 4, 5)
rownames(data2) <- c("C", "D", "B", "E")

# Get data1 into the same order as data2
data1[match(rownames(data2), data1$ids), ]

# Or data2 into the same order as data1
data2[match(data1$ids, rownames(data2)), ]

# This kind of works, in that it makes the rows in data1 match data2 where it can
# But we get NAs in each because some ids in data1 aren't in data2 and vice versa


# We can extract the rows from data1 and data2 that only have ids in common
data1_update <- subset(data1, ids %in% rownames(data2))
data2_update <- data2[rownames(data2) %in% data1$ids, ]

# Now we can try using match again

# Get data1_update into the same order as data2_update
data1_update[match(rownames(data2_update), data1_update$ids), ]

# Or data2_update into the same order as data1_update
data2_update[match(data1_update$ids, rownames(data2_update)), ]

# So ultimately we want to have two dataframes
# They have the same number of rows
# And the ids all match
data1 <- data1_update[match(rownames(data2_update), data1_update$ids), ]
data2 <- data2_update

save(data1, data2, file="some_file.RData")