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 matrices in a list according to the interactions attributes of the list.

Usage

OrientateMatrix(mtx, verbose = TRUE)

Arguments

mtx

<matrix or Listmatrix>: Matrix or matricies list to oriente

verbose

: Report the number of matrices corrected. (Default: TRUE)

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(
    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"
)

# Matrices Orientation
oriented_Interactions_PF.mtx_lst <- OrientateMatrix(interactions_PF.mtx_lst)
#> 794 matrices are oriented