The code below reeks of a misconception that lists are efficient to add
items to, which is a confusion with the computer science term "linked
list". In R, a list is NOT a linked list... it is a vector, which means
the memory used by the list is allocated at the time it is created, and
REALLOCATED when a new item is added. The only reason you should use a
list is because you expect to put values of different types or shapes into
it, which does not appear to apply in this use case.
In R, you should make a valiant effort to create things right the first
time, and if that doesn't work then preallocate the space you will need in
the vectors you are working with. Since you have a need to store a
variable number of elements in each intersectX element, the column needs
to be a list but the elements of that list can perfectly well be character
vectors.
x <- data.frame( TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA")
, CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2")
, POSA=c(10, 15, 120, 340, 100, 220)
, CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1")
, POSB=c(30, 100, 300, 20, 200, 320)
, stringsAsFactors = FALSE
)
compareRng <- function( chr1, pos1, chr2, pos2, delta ) {
( chr1 == chr2
& ( pos2 - delta ) < pos1
& pos1 < ( pos2 + delta )
)
}
makeIntersectX <- function( n, chrlabel, poslabel, delta ) {
lgclidx <- rep( TRUE, nrow( x ) )
lgclidx[ n ] <- FALSE
x[[ chrlabel ]][ compareRng( x[[ chrlabel ]][ n ]
, x[[ poslabel ]][ n ]
, x[[ chrlabel ]]
, x[[ poslabel ]]
, delta
)
& lgclidx
]
}
x$intersectA <- lapply( seq.int( nrow( x ) )
, makeIntersectX
, chrlabel = "CHRA"
, poslabel = "POSA"
, delta = 10L
)
x$intersectB <- lapply( seq.int( nrow( x ) )
, makeIntersectX
, chrlabel = "CHRB"
, poslabel = "POSB"
, delta = 21L
)
x
TYPE CHRA POSA CHRB POSB intersectA intersectB
1 DEL chr1 10 chr1 30 chr1
2 DEL chr1 15 chr1 100 chr1
3 DUP chr1 120 chr1 300 chr1
4 TRA chr1 340 chr2 20
5 INV chr2 100 chr2 200
6 TRA chr2 220 chr1 320 chr1
Note that depending on what you plan to do beyond this point, it might
actually be more performant to use a data frame with repeated rows instead
of list columns... but I cannot tell from what you have provided.
On Wed, 25 Jul 2018, Bogdan Tanasa wrote:
Dear Thierry and Juan, thank you for your help. Thank you all.
Now, if I would like to add an element to the empty list, how shall I do :
for example, shall i = 2, and j = 1, in a bit of more complex R code :
x <- data.frame(TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA"),
CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2"),
POSA=c(10, 15, 120, 340, 100, 220),
CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1"),
POSB=c(30, 100, 300, 20, 200, 320))
x$labA <- paste(x$CHRA, x$POSA, sep="_")
x$labB <- paste(x$CHRB, x$POSB, sep="_")
x$POSA_left <- x$POSA - 10
x$POSA_right <- x$POSA + 10
x$POSB_left <- x$POSB - 10
x$POSB_right <- x$POSB + 10
x$intersectA <- rep(list(list()), nrow(x))
x$intersectB <- rep(list(list()), nrow(x))
And we know that for i = 2, and j = 1, the condition is TRUE :
i <- 2
j <- 1
if ( (x$CHRA[i] == x$CHRA[j] ) &&
(x$POSA[i] > x$POSA_left[j] ) &&
(x$POSA[i] < x$POSA_right[j] ) ){
x$intersectA[i] <- c(x$intersectA[i], x$labA[j])}
the R code does not work. Thank you for your kind help !
On Wed, Jul 25, 2018 at 12:26 AM, Thierry Onkelinx <thierry.onkel...@inbo.be
wrote:
Dear Bogdan,
You are looking for x$intersectA <- vector("list", nrow(x))
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88
<https://maps.google.com/?q=Havenlaan+88&entry=gmail&source=g> bus 73,
1000 Brussel
www.inbo.be
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2018-07-25 8:55 GMT+02:00 Bogdan Tanasa <tan...@gmail.com>:
Dear all,
assuming that I do have a dataframe like :
x <- data.frame(TYPE=c("DEL", "DEL", "DUP", "TRA", "INV", "TRA"),
CHRA=c("chr1", "chr1", "chr1", "chr1", "chr2", "chr2"),
POSA=c(10, 15, 120, 340, 100, 220),
CHRB=c("chr1", "chr1", "chr1", "chr2", "chr2", "chr1"),
POSB=c(30, 100, 300, 20, 200, 320)) ,
how could I initiate another 2 columns in x, where each element in these 2
columns is going to be a list (the list could be updated later). Thank
you !
Shall I do,
for (i in 1:dim(x)[1]) { x$intersectA[i] <- list()}
for (i in 1:dim(x)[1]) { x$intersectB[i] <- list()}
nothing is happening. Thank you very much !
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