Converting unique strings to unique numbers

On Fri, May 29, 2015 at 2:16 PM, Herv? Pag?s <hpages at fredhutch.org> wrote:

Hi Kate,

I found that matching the character vector to itself is a very
effective way to do this:

   x <- c("a", "bunch", "of", "strings", "whose", "exact", "content",
          "is", "of", "little", "interest")
   ids <- match(x, x)
   ids
   # [1]  1  2  3  4  5  6  7  8  3 10 11

By using this trick, many manipulations on character vectors can
be replaced by manipulations on integer vectors, which are sometimes
way more efficient.

Hm. I hadn't thought of that approach - I use the
as.numeric(factor(...)) approach.

So I was curious, and compared the two:


set.seed(43)
x <- sample(letters, 10000, replace=TRUE)

system.time({
   for(i in seq_len(20000)) {
   ids1 <- match(x, x)
}})

#   user  system elapsed
#  9.657   0.000   9.657

system.time({
   for(i in seq_len(20000)) {
   ids2 <- as.numeric(factor(x, levels=letters))
}})

#   user  system elapsed
#   6.16    0.00    6.16

Using factor() is faster.

More importantly, using factor() lets you
set the order of the indices in an expected fashion, where match()
assigns them in the order of occurrence.

head(data.frame(x, ids1, ids2))

   x ids1 ids2
1 m    1   13
2 x    2   24
3 b    3    2
4 s    4   19
5 i    5    9
6 o    6   15

In a problem like Kate's where there are several columns for which the
same ordering of indices is desired, that becomes really important.

If you take Bill Dunlap's modification of the match() approach, it
resolves both problems: matching against the pooled unique values is
both faster than the factor() version and gives the same result:


On Fri, May 29, 2015 at 1:31 PM, William Dunlap <wdunlap at tibco.com> wrote:

match() will do what you want.  E.g., run your data through
the following function.

f <- function (data)
{
     uniqStrings <- unique(c(data[, 2], data[, 3], data[, 4]))
     uniqStrings <- setdiff(uniqStrings, "0")
     for (j in 2:4) {
         data[[j]] <- match(data[[j]], uniqStrings, nomatch = 0L)
     }
     data
}

##

y <- data.frame(id = 1:5000, v1 = sample(letters, 5000, replace=TRUE),
v2 = sample(letters, 5000, replace=TRUE), v3 = sample(letters, 5000,
replace=TRUE), stringsAsFactors=FALSE)


system.time({
   for(i in seq_len(20000)) {
     ids3 <- f(data.frame(y))
}})

#   user  system elapsed
# 22.515   0.000  22.518



ff <- function(data)
{
     uniqStrings <- unique(c(data[, 2], data[, 3], data[, 4]))
     uniqStrings <- setdiff(uniqStrings, "0")
     for (j in 2:4) {
         data[[j]] <- as.numeric(factor(data[[j]], levels=uniqStrings))
     }
     data
}

system.time({
   for(i in seq_len(20000)) {
     ids4 <- ff(data.frame(y))
}})

#    user  system elapsed
#  26.083   0.002  26.090

head(ids3)

   id v1 v2 v3
1  1  1  2  8
2  2  2 19 22
3  3  3 21 16
4  4  4 10 17
5  5  1  8 18
6  6  1 12 26

head(ids4)

   id v1 v2 v3
1  1  1  2  8
2  2  2 19 22
3  3  3 21 16
4  4  4 10 17
5  5  1  8 18
6  6  1 12 26

Kate, if you're getting all zeros, check str(yourdataframe) - it's
likely that when you imported your data into R the strings were
already converted to factors, which is not what you want (ask me how I
know this!).

Sarah

On 05/29/2015 09:58 AM, Kate Ignatius wrote:

I have a pedigree file as so:

X0001 BYX859      0      0  2  1 BYX859
X0001 BYX894      0      0  1  1 BYX894
X0001 BYX862 BYX894 BYX859  2  2 BYX862
X0001 BYX863 BYX894 BYX859  2  2 BYX863
X0001 BYX864 BYX894 BYX859  2  2 BYX864
X0001 BYX865 BYX894 BYX859  2  2 BYX865

And I was hoping to change all unique string values to numbers.

That is:

BYX859 = 1
BYX894 = 2
BYX862 = 3
BYX863 = 4
BYX864 = 5
BYX865 = 6

But only in columns 2 - 4.  Essentially I would like the data to look like
this:

X0001 1 0 0  2  1 BYX859
X0001 2 0 0  1  1 BYX894
X0001 3 2 1  2  2 BYX862
X0001 4 2 1  2  2 BYX863
X0001 5 2 1  2  2 BYX864
X0001 6 2 1  2  2 BYX865

Is this possible with factors?

Thanks!

K.