baboon2010
2011-Apr-20 09:01 UTC
[R] 'Record' row values every time the binary value in a collumn changes
My question is twofold.
Part 1:
My data looks like this:
(example set, real data has 2*10^6 rows)
binary<-c(1,1,1,0,0,0,1,1,1,0,0)
Chromosome<-c(1,1,1,1,1,1,2,2,2,2,2)
start<-c(12,17,18,20,25,36,12,15,16,17,19)
Table<-cbind(Chromosome,start,binary)
Chromosome start binary
[1,] 1 12 1
[2,] 1 17 1
[3,] 1 18 1
[4,] 1 20 0
[5,] 1 25 0
[6,] 1 36 0
[7,] 2 12 1
[8,] 2 15 1
[9,] 2 16 1
[10,] 2 17 0
[11,] 2 19 0
As output I need a shortlist for each binary block: giving me the starting
and ending position of each block.
Which for these example would look like this:
Chromosome2 position_start position_end binary2
[1,] 1 12 18 1
[2,] 1 20 36 0
[3,] 2 12 16 1
[4,] 2 17 19 0
Part 2:
Based on the output of part 1, I need to assign the binary to rows of
another data set. If the position value in this second data set falls in one
of the blocks defined in the shortlist made in part1,the binary value of the
shortlist should be assigned to an extra column for this row. This would
look something like this:
Chromosome3 position Value binary3
[1,] "1" "12" "a" "1"
[2,] "1" "13" "b" "1"
[3,] "1" "14" "c" "1"
[4,] "1" "15" "d" "1"
[5,] "1" "16" "e" "1"
[6,] "1" "18" "f" "1"
[7,] "1" "20" "g" "0"
[8,] "1" "21" "h" "0"
[9,] "1" "22" "i" "0"
[10,] "1" "23" "j" "0"
[11,] "1" "25" "k" "0"
[12,] "1" "35" "l" "0"
[13,] "2" "12" "m" "1"
[14,] "2" "13" "n" "1"
[15,] "2" "14" "o" "1"
[16,] "2" "15" "p" "1"
[17,] "2" "16" "q" "1"
[18,] "2" "17" "s" "0"
[19,] "2" "18" "d" "0"
[20,] "2" "19" "f" "0"
Many thanks in advance,
Niels
--
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jim holtman
2011-Apr-20 16:59 UTC
[R] 'Record' row values every time the binary value in a collumn changes
Here is an answer to part 1:> binary<-c(1,1,1,0,0,0,1,1,1,0,0) > Chromosome<-c(1,1,1,1,1,1,2,2,2,2,2) > start<-c(12,17,18,20,25,36,12,15,16,17,19) > Table<-cbind(Chromosome,start,binary) > # determine where the start/end of each group is > # use indices since the size is large > startEnd <- lapply(split(seq(nrow(Table))+ , list(Table[, "Chromosome"], Table[, 'binary']) + , drop = TRUE + ) + , function(.indx){ + se <- range(.indx) + c(Chromosome2 = unname(Table[se[1L], "Chromosome"]) + , position_start = unname(Table[se[1L], 'start']) + , position_end = unname(Table[se[2L], 'start']) + , binary2 = unname(Table[se[1L], 'binary']) + ) + })> do.call(rbind, startEnd)Chromosome2 position_start position_end binary2 1.0 1 20 36 0 2.0 2 17 19 0 1.1 1 12 18 1 2.1 2 12 16 1> >On Wed, Apr 20, 2011 at 5:01 AM, baboon2010 <nielsvanderaa at live.be> wrote:> My question is twofold. > > Part 1: > My data looks like this: > > (example set, real data has 2*10^6 rows) > binary<-c(1,1,1,0,0,0,1,1,1,0,0) > Chromosome<-c(1,1,1,1,1,1,2,2,2,2,2) > start<-c(12,17,18,20,25,36,12,15,16,17,19) > Table<-cbind(Chromosome,start,binary) > ? ? ?Chromosome start binary > ?[1,] ? ? ? ? ?1 ? ?12 ? ? ?1 > ?[2,] ? ? ? ? ?1 ? ?17 ? ? ?1 > ?[3,] ? ? ? ? ?1 ? ?18 ? ? ?1 > ?[4,] ? ? ? ? ?1 ? ?20 ? ? ?0 > ?[5,] ? ? ? ? ?1 ? ?25 ? ? ?0 > ?[6,] ? ? ? ? ?1 ? ?36 ? ? ?0 > ?[7,] ? ? ? ? ?2 ? ?12 ? ? ?1 > ?[8,] ? ? ? ? ?2 ? ?15 ? ? ?1 > ?[9,] ? ? ? ? ?2 ? ?16 ? ? ?1 > [10,] ? ? ? ? ?2 ? ?17 ? ? ?0 > [11,] ? ? ? ? ?2 ? ?19 ? ? ?0 > > As output I need a shortlist for each binary block: giving me the starting > and ending position of each block. > Which for these example would look like this: > ? ? Chromosome2 position_start position_end binary2 > [1,] ? ? ? ? ? 1 ? ? ? ? ? ? 12 ? ? ? ? ? 18 ? ? ? 1 > [2,] ? ? ? ? ? 1 ? ? ? ? ? ? 20 ? ? ? ? ? 36 ? ? ? 0 > [3,] ? ? ? ? ? 2 ? ? ? ? ? ? 12 ? ? ? ? ? 16 ? ? ? 1 > [4,] ? ? ? ? ? 2 ? ? ? ? ? ? 17 ? ? ? ? ? 19 ? ? ? 0 > > Part 2: > Based on the output of part 1, I need to assign the binary to rows of > another data set. If the position value in this second data set falls in one > of the blocks defined in the shortlist made in part1,the binary value of the > shortlist should be assigned to an extra column for this row. ?This would > look something like this: > ? ? Chromosome3 position Value binary3 > ?[1,] "1" ? ? ? ? "12" ? ? "a" ? "1" > ?[2,] "1" ? ? ? ? "13" ? ? "b" ? "1" > ?[3,] "1" ? ? ? ? "14" ? ? "c" ? "1" > ?[4,] "1" ? ? ? ? "15" ? ? "d" ? "1" > ?[5,] "1" ? ? ? ? "16" ? ? "e" ? "1" > ?[6,] "1" ? ? ? ? "18" ? ? "f" ? "1" > ?[7,] "1" ? ? ? ? "20" ? ? "g" ? "0" > ?[8,] "1" ? ? ? ? "21" ? ? "h" ? "0" > ?[9,] "1" ? ? ? ? "22" ? ? "i" ? "0" > [10,] "1" ? ? ? ? "23" ? ? "j" ? "0" > [11,] "1" ? ? ? ? "25" ? ? "k" ? "0" > [12,] "1" ? ? ? ? "35" ? ? "l" ? "0" > [13,] "2" ? ? ? ? "12" ? ? "m" ? "1" > [14,] "2" ? ? ? ? "13" ? ? "n" ? "1" > [15,] "2" ? ? ? ? "14" ? ? "o" ? "1" > [16,] "2" ? ? ? ? "15" ? ? "p" ? "1" > [17,] "2" ? ? ? ? "16" ? ? "q" ? "1" > [18,] "2" ? ? ? ? "17" ? ? "s" ? "0" > [19,] "2" ? ? ? ? "18" ? ? "d" ? "0" > [20,] "2" ? ? ? ? "19" ? ? "f" ? "0" > > > Many thanks in advance, > > Niels > > -- > View this message in context: http://r.789695.n4.nabble.com/Record-row-values-every-time-the-binary-value-in-a-collumn-changes-tp3462496p3462496.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > R-help at r-project.org mailing list > 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. >-- Jim Holtman Data Munger Guru What is the problem that you are trying to solve?
Dennis Murphy
2011-Apr-20 17:39 UTC
[R] 'Record' row values every time the binary value in a collumn changes
Hi:
Here are a couple more options using packages plyr and data.table. The
labels in the second part are changed because they didn't make sense
in a 2M line file (well, mine may not either, but it's a start). You
can always change them to something more pertinent.
# Question 1:
Table <- data.frame(binary, chromosome = Chromosome, start)
library(plyr)
(df <- ddply(Table, .(chromosome, binary), summarise, position_start
min(start),
position_end = max(start)))
chromosome binary position_start position_end
1 1 0 20 36
2 1 1 12 18
3 2 0 17 19
4 2 1 12 16
library(data.table)
dTable <- data.table(Table, key = 'chromosome, binary')
(dt <- dTable[, list(position_start = min(start),
position_end = max(start)), by = 'chromosome, binary'])
chromosome binary position_start position_end
[1,] 1 0 20 36
[2,] 1 1 12 18
[3,] 2 0 17 19
[4,] 2 1 12 16
## Question 2:
For plyr, it's easy to write a function that takes a generic input data
frame
(in this case, a single line) and then outputs a data frame with
positions and labels.
tfun <- function(df) {
diff <- with(df, position_end - position_start + 1)
position <- with(df, seq(position_start, position_end))
value <- paste(df$chromosome, df$binary, letters[1:diff], sep =
'.')
data.frame(chromosome = df$chromosome, position, value, binary = df$binary)
}
# Then:
> ddply(df, .(chromosome, binary), tfun)
chromosome position value binary
1 1 20 1.0.a 0
2 1 21 1.0.b 0
3 1 22 1.0.c 0
4 1 23 1.0.d 0
5 1 24 1.0.e 0
6 1 25 1.0.f 0
7 1 26 1.0.g 0
8 1 27 1.0.h 0
9 1 28 1.0.i 0
10 1 29 1.0.j 0
11 1 30 1.0.k 0
12 1 31 1.0.l 0
13 1 32 1.0.m 0
14 1 33 1.0.n 0
15 1 34 1.0.o 0
16 1 35 1.0.p 0
17 1 36 1.0.q 0
18 1 12 1.1.a 1
19 1 13 1.1.b 1
20 1 14 1.1.c 1
21 1 15 1.1.d 1
22 1 16 1.1.e 1
23 1 17 1.1.f 1
24 1 18 1.1.g 1
25 2 17 2.0.a 0
26 2 18 2.0.b 0
27 2 19 2.0.c 0
28 2 12 2.1.a 1
29 2 13 2.1.b 1
30 2 14 2.1.c 1
31 2 15 2.1.d 1
32 2 16 2.1.e 1
# For data.table, one can apply the internals of tfun directly:
dt[, list(chromosome = chromosome, position = seq(position_start, position_end),
value = paste(chromosome, binary,
letters[1:(position_end - position_start + 1)],
sep = '.'),
binary = binary), by = 'chromosome, binary']
chromosome binary chromosome.1 position value binary.1
1 0 1 20 1.0.a 0
1 0 1 21 1.0.b 0
1 0 1 22 1.0.c 0
1 0 1 23 1.0.d 0
1 0 1 24 1.0.e 0
1 0 1 25 1.0.f 0
1 0 1 26 1.0.g 0
1 0 1 27 1.0.h 0
1 0 1 28 1.0.i 0
1 0 1 29 1.0.j 0
1 0 1 30 1.0.k 0
1 0 1 31 1.0.l 0
1 0 1 32 1.0.m 0
1 0 1 33 1.0.n 0
1 0 1 34 1.0.o 0
1 0 1 35 1.0.p 0
1 0 1 36 1.0.q 0
1 1 1 12 1.1.a 1
1 1 1 13 1.1.b 1
1 1 1 14 1.1.c 1
1 1 1 15 1.1.d 1
1 1 1 16 1.1.e 1
1 1 1 17 1.1.f 1
1 1 1 18 1.1.g 1
2 0 2 17 2.0.a 0
2 0 2 18 2.0.b 0
2 0 2 19 2.0.c 0
2 1 2 12 2.1.a 1
2 1 2 13 2.1.b 1
2 1 2 14 2.1.c 1
2 1 2 15 2.1.d 1
2 1 2 16 2.1.e 1
cn chromosome binary chromosome position value binary
HTH,
Dennis
On Wed, Apr 20, 2011 at 2:01 AM, baboon2010 <nielsvanderaa at live.be>
wrote:> My question is twofold.
>
> Part 1:
> My data looks like this:
>
> (example set, real data has 2*10^6 rows)
> binary<-c(1,1,1,0,0,0,1,1,1,0,0)
> Chromosome<-c(1,1,1,1,1,1,2,2,2,2,2)
> start<-c(12,17,18,20,25,36,12,15,16,17,19)
> Table<-cbind(Chromosome,start,binary)
> ? ? ?Chromosome start binary
> ?[1,] ? ? ? ? ?1 ? ?12 ? ? ?1
> ?[2,] ? ? ? ? ?1 ? ?17 ? ? ?1
> ?[3,] ? ? ? ? ?1 ? ?18 ? ? ?1
> ?[4,] ? ? ? ? ?1 ? ?20 ? ? ?0
> ?[5,] ? ? ? ? ?1 ? ?25 ? ? ?0
> ?[6,] ? ? ? ? ?1 ? ?36 ? ? ?0
> ?[7,] ? ? ? ? ?2 ? ?12 ? ? ?1
> ?[8,] ? ? ? ? ?2 ? ?15 ? ? ?1
> ?[9,] ? ? ? ? ?2 ? ?16 ? ? ?1
> [10,] ? ? ? ? ?2 ? ?17 ? ? ?0
> [11,] ? ? ? ? ?2 ? ?19 ? ? ?0
>
> As output I need a shortlist for each binary block: giving me the starting
> and ending position of each block.
> Which for these example would look like this:
> ? ? Chromosome2 position_start position_end binary2
> [1,] ? ? ? ? ? 1 ? ? ? ? ? ? 12 ? ? ? ? ? 18 ? ? ? 1
> [2,] ? ? ? ? ? 1 ? ? ? ? ? ? 20 ? ? ? ? ? 36 ? ? ? 0
> [3,] ? ? ? ? ? 2 ? ? ? ? ? ? 12 ? ? ? ? ? 16 ? ? ? 1
> [4,] ? ? ? ? ? 2 ? ? ? ? ? ? 17 ? ? ? ? ? 19 ? ? ? 0
>
> Part 2:
> Based on the output of part 1, I need to assign the binary to rows of
> another data set. If the position value in this second data set falls in
one
> of the blocks defined in the shortlist made in part1,the binary value of
the
> shortlist should be assigned to an extra column for this row. ?This would
> look something like this:
> ? ? Chromosome3 position Value binary3
> ?[1,] "1" ? ? ? ? "12" ? ? "a" ?
"1"
> ?[2,] "1" ? ? ? ? "13" ? ? "b" ?
"1"
> ?[3,] "1" ? ? ? ? "14" ? ? "c" ?
"1"
> ?[4,] "1" ? ? ? ? "15" ? ? "d" ?
"1"
> ?[5,] "1" ? ? ? ? "16" ? ? "e" ?
"1"
> ?[6,] "1" ? ? ? ? "18" ? ? "f" ?
"1"
> ?[7,] "1" ? ? ? ? "20" ? ? "g" ?
"0"
> ?[8,] "1" ? ? ? ? "21" ? ? "h" ?
"0"
> ?[9,] "1" ? ? ? ? "22" ? ? "i" ?
"0"
> [10,] "1" ? ? ? ? "23" ? ? "j" ?
"0"
> [11,] "1" ? ? ? ? "25" ? ? "k" ?
"0"
> [12,] "1" ? ? ? ? "35" ? ? "l" ?
"0"
> [13,] "2" ? ? ? ? "12" ? ? "m" ?
"1"
> [14,] "2" ? ? ? ? "13" ? ? "n" ?
"1"
> [15,] "2" ? ? ? ? "14" ? ? "o" ?
"1"
> [16,] "2" ? ? ? ? "15" ? ? "p" ?
"1"
> [17,] "2" ? ? ? ? "16" ? ? "q" ?
"1"
> [18,] "2" ? ? ? ? "17" ? ? "s" ?
"0"
> [19,] "2" ? ? ? ? "18" ? ? "d" ?
"0"
> [20,] "2" ? ? ? ? "19" ? ? "f" ?
"0"
>
>
> Many thanks in advance,
>
> Niels
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/Record-row-values-every-time-the-binary-value-in-a-collumn-changes-tp3462496p3462496.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.
>