Search in a GInteraction object which interactions correspond to a target list and return a list of index or filter a matrices list according to target and a selectionFunction.
Usage
FilterInteractions(
matrices = NULL,
genomicInteractions = NULL,
targets = NULL,
selectionFun = function() {
Reduce(intersect, interarctions.ndx_lst)
}
)Arguments
- matrices
<Listmatrix>: The matrices list to filter. If is not
NULL, the function will return the filtred matrices list, else it will return a list of index.- genomicInteractions
: The GInteraction object on which to compute the filter. - targets
- : A named list that describe the target.
- selectionFun
: A function that defines how the target variables must be crossed. (Default intersection of all targets)
Examples
# Data
data(Beaf32_Peaks.gnr)
data(HiC_Ctrl.cmx_lst)
# Index Beaf32
Beaf32_Index.gnr <- IndexFeatures(
gRangeList = list(Beaf = Beaf32_Peaks.gnr),
chromSizes = data.frame(seqnames = c("2L", "2R"),
seqlengths = c(23513712, 25286936)),
binSize = 100000
)
# Beaf32 <-> Beaf32 Pairing
Beaf_Beaf.gni <- SearchPairs(indexAnchor = Beaf32_Index.gnr)
Beaf_Beaf.gni <- Beaf_Beaf.gni[seq_len(2000)] # subset 2000 first for exemple
# Matrices extractions center on Beaf32 <-> Beaf32 point interaction
interactions_PF.mtx_lst <- ExtractSubmatrix(
genomicFeature = Beaf_Beaf.gni,
hicLst = HiC_Ctrl.cmx_lst,
referencePoint = "pf"
)
# Create a target
targets <- list(
anchor.Beaf.name = c("Beaf32_108", "Beaf32_814"),
distance = function(dist) {
dist < 300000
}
)
# We target the Beaf32<->Beaf32 interactions that are less than 300Kb away
# and have peak Beaf32_2 and Beaf32_191 as anchors (i.e. left).
# Create a selection
selectionFun <- function() {
intersect(anchor.Beaf.name, distance)
}
# We select the Beaf32<->Beaf32 interactions that satisfy both targeting
# criteria (intersection).
# Filtration on InteractionSet (Beaf32 <-> Beaf32 Pairs)
FilterInteractions(
genomicInteractions = Beaf_Beaf.gni,
targets = targets,
selectionFun = NULL
) |> str(max.level = 1)
#> List of 2
#> $ anchor.Beaf.name: int [1:25] 9 77 144 212 278 346 411 479 543 611 ...
#> $ distance : int [1:24] 1 2 137 138 272 273 406 407 539 540 ...
# Returns a named list (the names match the targeting criteria).
# Each element is an index vector of Beaf32<->Beaf32 interactions
# that satisfy the given criteria.
# Filtration on Matrices List (Beaf32 <-> Beaf32 Extracted matrices)
FilterInteractions(
matrices = interactions_PF.mtx_lst,
targets = targets,
selectionFun = NULL
) |> str(max.level = 1)
#> List of 2
#> $ anchor.Beaf.name: int [1:7] 68 191 313 434 554 673 791
#> $ distance : int [1:8] 1 370 491 492 611 612 730 731
# Return the same kind of result.
# Add the selection on InteractionSet Filtration
FilterInteractions(
genomicInteractions = Beaf_Beaf.gni,
targets = targets,
selectionFun = selectionFun
) |> str(max.level = 1)
#> int 1061
# This return the intersection of the index vector that satisfy both
# targeting criteria.
# Add the selection on Matrices List Filtration
FilterInteractions(
matrices = interactions_PF.mtx_lst,
targets = targets,
selectionFun = selectionFun
) |> str(max.level = 1)
#> Named list()
#> - attr(*, "interactions")=Formal class 'GInteractions' [package "InteractionSet"] with 6 slots
#> - attr(*, "resolution")= num 1e+05
#> - attr(*, "referencePoint")= chr "pf"
#> - attr(*, "matriceDim")= num 21
#> - attr(*, "target")=List of 2
#> - attr(*, "selection")=function ()
#> ..- attr(*, "srcref")= 'srcref' int [1:8] 35 17 37 1 17 1 35 37
#> .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x555d8bfecd70>
# This return the filtred matrices, i.e the matrices for which
# the Beaf32<->Beaf32 interactions satisfy both targeting criteria.
# Filtration with InteractionsSet as filtration criteria
targets <- list(interactions = Beaf_Beaf.gni[seq_len(2)])
FilterInteractions(
genomicInteractions = Beaf_Beaf.gni,
targets = targets,
selectionFun = NULL
) |> str(max.level = 1)
#> Named int [1:2] 1 2
#> - attr(*, "names")= chr [1:2] "interactions1" "interactions2"
# Filtration with GRanges as filtration criteria
targets <- list(first =
InteractionSet::anchors(Beaf_Beaf.gni)[["first"]][seq_len(2)])
FilterInteractions(
genomicInteractions = Beaf_Beaf.gni,
targets = targets,
selectionFun = NULL
) |> str(max.level = 1)
#> Named int [1:3] 1 2 137
#> - attr(*, "names")= chr [1:3] "first1" "first2" "first3"