Matrix orientation

Oriente extracted Matrix according to the anchors and bait order. Apply a 180° rotation follow with a transposation on a matrix or on matricies in a list according to the interactions attributes of the list.

Usage

OrientateMatrix(matrice.mtx)

Arguments

matrice.mtx

<matrix or List[matrix]>: Matrix or matricies list to oriente

Value

Oriented matrix or matricies list

Details

OrientateMatrix

Examples

# Data
data(Beaf32_Peaks.gnr)
data(HiC_Ctrl.cmx_lst)

# Index Beaf32 in TADs domains
Beaf32_Index.gnr <- IndexFeatures(
    gRange.gnr_lst = list(Beaf = Beaf32_Peaks.gnr),
    chromSize.dtf = data.frame(
        seqnames = c("2L", "2R"),
        seqlengths = c(23513712, 25286936)
    ),
    binSize.num = 100000
)

# Beaf32 <-> Beaf32 Pairing
Beaf_Beaf.gni <- SearchPairs(indexAnchor.gnr = 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(
    feature.gn = Beaf_Beaf.gni,
    hic.cmx_lst = HiC_Ctrl.cmx_lst,
    referencePoint.chr = "pf"
)

# Matrices Orientation
oriented_Interactions_PF.mtx_lst <- OrientateMatrix(interactions_PF.mtx_lst)
#> 677 matrices are oriented