Calculate loop enrichment over background.
Source:R/AllGenerics.R, R/methods-calcLoopEnrichment.R
calcLoopEnrichment.RdPulls Hi-C pixels and calculates the enrichment of the selected foreground (`fg`) over the selected background (`bg`).
Usage
calcLoopEnrichment(
x,
files,
fg = selectCenterPixel(mhDist = 1, buffer = defaultBuffer()),
bg = selectTopLeft(n = 4, buffer = defaultBuffer()) + selectBottomRight(n = 4, buffer =
defaultBuffer()),
FUN = function(fg, bg) median(fg + 1)/median(bg + 1),
nBlocks = 5,
verbose = TRUE,
BPPARAM = bpparam(),
...
)
# S4 method for GInteractions,character
calcLoopEnrichment(
x,
files,
fg = selectCenterPixel(mhDist = 1, buffer = defaultBuffer()),
bg = selectTopLeft(n = 4, buffer = defaultBuffer()) + selectBottomRight(n = 4, buffer =
defaultBuffer()),
FUN = function(fg, bg) median(fg + 1)/median(bg + 1),
nBlocks = 5,
verbose = TRUE,
BPPARAM = bpparam(),
...
)
# S4 method for InteractionArray,missing
calcLoopEnrichment(
x,
files,
fg = selectCenterPixel(mhDist = 1, buffer = defaultBuffer()),
bg = selectTopLeft(n = 4, buffer = defaultBuffer()) + selectBottomRight(n = 4, buffer =
defaultBuffer()),
FUN = function(fg, bg) median(fg + 1)/median(bg + 1),
nBlocks = 5,
verbose = TRUE,
BPPARAM = bpparam(),
...
)Arguments
- x
GInteractions object or an InteractionArray object.
- files
Character file paths to `.hic` files. Required only if GInteractions object is supplied for x.
- fg
MatrixSelection object of matrix indices for the foreground.
- bg
MatrixSelection object of matrix indices for the background.
- FUN
Function with at least two parameters (i.e., `fg`, `bg`) defining how enrichment should be calculated. Must produce a single value (numeric of length one). The first and second parameters must represent fg and bg, respectively.
- nBlocks
Number of blocks for block-processing arrays. Default is 5. Increase this for large datasets. To read and process all data at once, set this value to 1.
- verbose
Boolean (TRUE or FALSE) describing whether to report block-processing progress.
- BPPARAM
Parallelization params (passed to `BiocParallel::bplapply()`). Default is the result of `BiocParallel::bpparams()`. Parallel processing is not available when `by=interactions`.
- ...
Additional arguments passed to `pullHicMatrices`. See ?[`pullHicMatrices`].
Value
A DelayedMatrix of enrichment scores where rows are interactions (i.e. loops) and columns are Hi-C files.
Examples
## Load marinerData
if (!require("marinerData", quietly = TRUE))
BiocManager::install("marinerData")
## Read .hic file paths
hicFiles <- c(
marinerData::LEUK_HEK_PJA27_inter_30.hic(),
marinerData::LEUK_HEK_PJA30_inter_30.hic()
)
#> see ?marinerData and browseVignettes('marinerData') for documentation
#> loading from cache
#> see ?marinerData and browseVignettes('marinerData') for documentation
#> loading from cache
names(hicFiles) <- c("FS", "WT")
## Read in loops as GInteractions object
loops <-
WT_5kbLoops.txt() |>
setNames("WT") |>
read.table(header=TRUE) |>
as_ginteractions(keep.extra.columns=FALSE)
#> see ?marinerData and browseVignettes('marinerData') for documentation
#> loading from cache
## Removes the "chr" prefix for compatibility
## with the preprocessed hic files
GenomeInfoDb::seqlevelsStyle(loops) <- 'ENSEMBL'
## Expand binSize of loops
loops <- assignToBins(x=loops, binSize=100e3)
## Calculate loop enrichment
calcLoopEnrichment(x=loops[1:10],
files=hicFiles)
#> '0' = foreground;
#> 'X' = background;
#> '*' = both;
#> '-' = unselected
#>
#> X X X X - - - - - - -
#> X X X X - - - - - - -
#> X X X X - - - - - - -
#> X X X X - - - - - - -
#> - - - - - 0 - - - - -
#> - - - - 0 0 0 - - - -
#> - - - - - 0 - - - - -
#> - - - - - - - X X X X
#> - - - - - - - X X X X
#> - - - - - - - X X X X
#> - - - - - - - X X X X
#> <10 x 2> DelayedMatrix object of type "double":
#> FS WT
#> [1,] 1.0000000 1.6666667
#> [2,] 1.0000000 1.4000000
#> [3,] 1.5789474 2.1666667
#> [4,] 1.3333333 1.0000000
#> [5,] 0.7368421 0.7777778
#> [6,] 1.3333333 1.0000000
#> [7,] 0.7500000 1.0000000
#> [8,] 1.7647059 1.4482759
#> [9,] 0.8181818 0.9090909
#> [10,] 0.3333333 0.8000000
## Customize different foreground/background
## with selection functions
buffer <- 10 # choose pixel radius around center
fg <- selectCenterPixel(mhDist=seq(0,4), buffer=buffer)
bg <- selectCorners(n=6, buffer=buffer) +
selectOuter(n=2, buffer=buffer)
## Calculate loop enrichment
calcLoopEnrichment(x=loops[1:10],
files=hicFiles,
fg=fg,
bg=bg)
#> '0' = foreground;
#> 'X' = background;
#> '*' = both;
#> '-' = unselected
#>
#> X X X X X X X X X X X X X X X X X X X X X
#> X X X X X X X X X X X X X X X X X X X X X
#> X X X X X X - - - - - - - - - X X X X X X
#> X X X X X X - - - - - - - - - X X X X X X
#> X X X X X X - - - - - - - - - X X X X X X
#> X X X X X X - - - - - - - - - X X X X X X
#> X X - - - - - - - - 0 - - - - - - - - X X
#> X X - - - - - - - 0 0 0 - - - - - - - X X
#> X X - - - - - - 0 0 0 0 0 - - - - - - X X
#> X X - - - - - 0 0 0 0 0 0 0 - - - - - X X
#> X X - - - - 0 0 0 0 0 0 0 0 0 - - - - X X
#> X X - - - - - 0 0 0 0 0 0 0 - - - - - X X
#> X X - - - - - - 0 0 0 0 0 - - - - - - X X
#> X X - - - - - - - 0 0 0 - - - - - - - X X
#> X X - - - - - - - - 0 - - - - - - - - X X
#> X X X X X X - - - - - - - - - X X X X X X
#> X X X X X X - - - - - - - - - X X X X X X
#> X X X X X X - - - - - - - - - X X X X X X
#> X X X X X X - - - - - - - - - X X X X X X
#> X X X X X X X X X X X X X X X X X X X X X
#> X X X X X X X X X X X X X X X X X X X X X
#> <10 x 2> DelayedMatrix object of type "double":
#> FS WT
#> [1,] 2.500000 2.000000
#> [2,] 2.666667 3.500000
#> [3,] 2.000000 2.500000
#> [4,] 2.000000 1.500000
#> [5,] 2.666667 3.000000
#> [6,] 3.000000 2.500000
#> [7,] 1.500000 1.500000
#> [8,] 6.000000 4.500000
#> [9,] 2.333333 1.250000
#> [10,] 1.000000 1.000000
## Extract count matrices first
mats <- assignToBins(loops[1:10],100e3) |>
pixelsToMatrices(buffer=10) |>
pullHicMatrices(
files=hicFiles,
binSize=100e3)
## Calculate loop enrichment from count matrices
calcLoopEnrichment(x = mats)
#> '0' = foreground;
#> 'X' = background;
#> '*' = both;
#> '-' = unselected
#>
#> X X X X - - - - - - - - - - - - - - - - -
#> X X X X - - - - - - - - - - - - - - - - -
#> X X X X - - - - - - - - - - - - - - - - -
#> X X X X - - - - - - - - - - - - - - - - -
#> - - - - - - - - - - - - - - - - - - - - -
#> - - - - - - - - - - - - - - - - - - - - -
#> - - - - - - - - - - - - - - - - - - - - -
#> - - - - - - - - - - - - - - - - - - - - -
#> - - - - - - - - - - - - - - - - - - - - -
#> - - - - - - - - - - 0 - - - - - - - - - -
#> - - - - - - - - - 0 0 0 - - - - - - - - -
#> - - - - - - - - - - 0 - - - - - - - - - -
#> - - - - - - - - - - - - - - - - - - - - -
#> - - - - - - - - - - - - - - - - - - - - -
#> - - - - - - - - - - - - - - - - - - - - -
#> - - - - - - - - - - - - - - - - - - - - -
#> - - - - - - - - - - - - - - - - - - - - -
#> - - - - - - - - - - - - - - - - - X X X X
#> - - - - - - - - - - - - - - - - - X X X X
#> - - - - - - - - - - - - - - - - - X X X X
#> - - - - - - - - - - - - - - - - - X X X X
#> <10 x 2> DelayedMatrix object of type "double":
#> FS WT
#> [1,] 0.8333333 1.1111111
#> [2,] 0.7142857 1.1666667
#> [3,] 1.7647059 2.0000000
#> [4,] 1.0000000 0.7500000
#> [5,] 0.7000000 0.7000000
#> [6,] 1.5000000 1.3333333
#> [7,] 1.0000000 1.2000000
#> [8,] 2.0689655 2.2105263
#> [9,] 0.6206897 0.7142857
#> [10,] 0.5000000 1.0000000