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 <gaiusjaugus...@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]]
>
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______________________________________________
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