[R] Efficient way to create new column based on comparison with another dataframe

[Dénes Tóth]

Hi,

I have not followed this thread from the beginning, but have you tried 
the foverlaps() function from the data.table package?

Something along the lines of:

---
# create the tables (use as.data.table() or setDT() if you
# start with a data.frame)
mapfile <- data.table(Name = c("S1", "S2", "S3"), Chr = 1,
                       Position = c(3000, 6000, 1000))
Chr.Arms <- data.table(Chr = 1, Arm = c("p", "q"),
                        Start = c(0, 5001), End = c(5000, 10000))

# add a dummy variable to be able to define Position as an interval
mapfile[, Position2 := Position]

# add keys
setkey(mapfile, Chr, Position, Position2)
setkey(Chr.Arms, Chr, Start, End)

# use data.table::foverlaps (see ?foverlaps)
mapfile <- foverlaps(mapfile, Chr.Arms, type = "within")

# remove the dummy variable
mapfile[, Position2 := NULL]

# recreate original order
setorder(mapfile, Chr, Name)

---

BTW, there is a typo in your *SOLUTION*. I guess you wanted to write 
data.table(Name = c("S1", "S2", "S3"), Chr = 1, Position = c(3000, 6000, 
1000), key = "Chr") instead of data.frame(Name = c("S1", "S2", "S3"), 
Chr = 1, Position = c(3000, 6000, 1000), key = "Chr").

HTH,
   Denes



On 01/30/2016 07:48 PM, Gaius Augustus wrote:
> I'll look into the Intervals idea.  The data.table code posted might not
> work (because I don't believe it would put the rows in the correct order if
> the chromosomes are interspersed), however, it did make me think about
> possibly assigning based on values...
>
> *SOLUTION*
> mapfile <- data.frame(Name = c("S1", "S2", "S3"), Chr = 1, Position =
> c(3000, 6000, 1000), key = "Chr")
> Chr.Arms <- data.frame(Chr = 1, Arm = c("p", "q"), Start = c(0, 5001), End
> = c(5000, 10000), key = "Chr")
>
> for(i in 1:nrow(Chr.Arms)){
>    cur.row <- Chr.Arms[i, ]
>    mapfile$Arm[ mapfile$Chr == cur.row$Chr & mapfile$Position >=
> cur.row$Start & mapfile$Position <= cur.row$End] <- cur.row$Arm
> }
>
> This took out the need for the intermediate table/vector.  This worked for
> me, and was VERY fast.  Took <5 minutes on a dataframe with 35 million rows.
>
> Thanks for the help,
> Gaius
>
> On Sat, Jan 30, 2016 at 10:50 AM, Gaius Augustus <gaiusjaugustus at gmail.com>
> wrote:
>
>> I'll look into the Intervals idea.  The data.table code posted might not
>> work (because I don't believe it would put the rows in the correct order if
>> the chromosomes are interspersed), however, it did make me think about
>> possibly assigning based on values...
>>
>> Something like:
>> mapfile <- data.table(Name = c("S1", "S2", "S3"), Chr = 1, Position =
>> c(3000, 6000, 1000), key = "Chr")
>> Chr.Arms <- data.table(Chr = 1, Arm = c("p", "q"), Start = c(0, 5001), End
>> = c(5000, 10000), key = "Chr")
>>
>> for(i in 1:nrow(Chr.Arms)){
>>    cur.row <- Chr.Arms[i, ]
>>    mapfile[ Chr == cur.row$Chr & Position >= cur.row$Start & Position <=
>> cur.row$End] <- Chr.Arms$Arm
>> }
>>
>> This might take out the need for the intermediate table/vector.  Not sure
>> yet if it'll work, but we'll see.  I'm interested to know if anyone else
>> has any ideas, too.
>>
>> Thanks,
>> Gaius
>>
>> On Fri, Jan 29, 2016 at 11:34 PM, Ulrik Stervbo <ulrik.stervbo at gmail.com>
>> wrote:
>>
>>> Hi Gaius,
>>>
>>> Could you use data.table and loop over the small Chr.arms?
>>>
>>> library(data.table)
>>> mapfile <- data.table(Name = c("S1", "S2", "S3"), Chr = 1, Position =
>>> c(3000, 6000, 1000), key = "Chr")
>>> Chr.Arms <- data.table(Chr = 1, Arm = c("p", "q"), Start = c(0, 5001),
>>> End = c(5000, 10000), key = "Chr")
>>>
>>> Arms <- data.table()
>>> for(i in 1:nrow(Chr.Arms)){
>>>    cur.row <- Chr.Arms[i, ]
>>>    Arm <- mapfile[ Position >= cur.row$Start & Position <= cur.row$End]
>>>    Arm <- Arm[ , Arm:=cur.row$Arm][]
>>>    Arms <- rbind(Arms, Arm)
>>> }
>>>
>>> # Or use plyr to loop over each possible arm
>>> library(plyr)
>>> Arms <- ddply(Chr.Arms, .variables = "Arm", function(cur.row, mapfile){
>>>    mapfile <- mapfile[ Position >= cur.row$Start & Position <= cur.row$End]
>>>    mapfile <- mapfile[ , Arm:=cur.row$Arm][]
>>>    return(mapfile)
>>> }, mapfile = mapfile)
>>>
>>> I have just started to use the data.table and I have the feeling the code
>>> above can be greatly improved - maybe the loop can be dropped entirely?
>>>
>>> Hope this helps
>>> Ulrik
>>>
>>> On Sat, 30 Jan 2016 at 03:29 Gaius Augustus <gaiusjaugustus at gmail.com>
>>> wrote:
>>>
>>>> I have two dataframes. One has chromosome arm information, and the other
>>>> has SNP position information. I am trying to assign each SNP an arm
>>>> identity.  I'd like to create this new column based on comparing it to
>>>> the
>>>> reference file.
>>>>
>>>> *1) Mapfile (has millions of rows)*
>>>>
>>>> Name    Chr   Position
>>>> S1      1      3000
>>>> S2      1      6000
>>>> S3      1      1000
>>>>
>>>> *2) Chr.Arms   file (has 39 rows)*
>>>>
>>>> Chr    Arm    Start   End
>>>> 1      p      0       5000
>>>> 1      q      5001    10000
>>>>
>>>>
>>>> *R Script that works, but slow:*
>>>> Arms  <- c()
>>>> for (line in 1:nrow(Mapfile)){
>>>>        Arms[line] <- Chr.Arms$Arm[ Mapfile$Chr[line] == Chr.Arms$Chr &
>>>>   Mapfile$Position[line] > Chr.Arms$Start &  Mapfile$Position[line] <
>>>> Chr.Arms$End]}
>>>> }
>>>> Mapfile$Arm <- Arms
>>>>
>>>>
>>>> *Output Table:*
>>>>
>>>> Name   Chr   Position   Arm
>>>> S1      1     3000      p
>>>> S2      1     6000      q
>>>> S3      1     1000      p
>>>>
>>>>
>>>> In words: I want each line to look up the location ( 1) find the right
>>>> Chr,
>>>> 2) find the line where the START < POSITION < END), then get the ARM
>>>> information and place it in a new column.
>>>>
>>>> This R script works, but surely there is a more time/processing efficient
>>>> way to do it.
>>>>
>>>> Thanks in advance for any help,
>>>> Gaius
>>>>
>>>>          [[alternative HTML version deleted]]
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide
>>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>
>>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>