Function that computes quantification of contact frequencies in a given area and returns it in a named vector.
Arguments
- matrices
<Listmatrix>: A matrices list.
- areaFun
: A character or function that allows to extract an area from each matrix that composes the matrices list (Default "center"). "C" or "CENTER": 3x3 pixels at the intersection between anchor and bait.
"UL" or "UPPER_LEFT": pixels in the uppper left square
"UR" or "UPPER_RIGHT": pixels in the uppper right square
"BL" or "BOTTOM_LEFT": pixels in the bottom left square
"BR" or "BOTTOM_RIGHT": pixels in the bottom right square
"U" or "UPPER": pixels above the center area
"B" or "BOTTOM": pixels below the center area
"L" or "LEFT": pixels in the left of the center area
"R" or "RIGHT": pixels in the right of the center area
"D" or "DONUT": pixels that surrounds the center area
- operationFun
: A character or function specifying the operation applied to the selected area. (Default "mean_rm0") "mean_rm0": apply a mean after replacing 0 with NA
"median_rm0": apply a median after replacing 0 with NA
"sum_rm0": apply a sum after replacing 0 with NA
"median": apply a median
"sum": apply a sum
"mean" or other character: apply a mean
- varName
: The name of a column in GInteraction attributes of matrices used as named in the output vector (Default NULL). By default, sub-matrices IDs are used.
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"
)
GetQuantif(
matrices = interactions_PF.mtx_lst,
areaFun = "center",
operationFun = "mean"
) |> head()
#> 2L:11_2L:12 2L:11_2L:17 2L:11_2L:20 2L:11_2L:22 2L:11_2L:23 2L:11_2L:24
#> 31422.8750 1866.5556 779.7778 788.0000 760.1111 554.1111