interactions2tads: Maps interactions to TADs.

In rz6/CopulaHiC: Hi-C differential analysis via dependency modelling of chromatin interactions with generalized linear models

Description

Maps cells of a contact map given in sparse format to TADs. User must provide interactions data frame and TADs for single and the same chromosome, otherwise the function will throw an error or behaviour will undefined.

Usage

interactions2tads(mtx.sparse, tads, cols = c("val"))

Arguments

mtx.sparse	data.frame with Hi-C contact map in sparse format; must have i and j columns, i.e. cell coordinates
tads	data frame containg TADs, for single chromosome; it is assumed that first TAD on every chromosome start at 0 and end of TAD equals start of next TAD (in case if there is no break between consecutive TADs); also user is responsible for converting TAD boundary coordinates to bins
cols	character vector with columns from mtx.sparse or tads data.frames to be included in resulting data frame; by default only val column is included

Value

data.frame with following columns: i, j, val, tad.id, start, end, name (and additional if cols specified), where each row corresponds to cell in Hi-C contact map with i, j coordinates and cells are assigned to TADs (cells which do not belong to any TAD are discarded)

Examples

# create artificial interactions set
sparse.mtx <- data.frame(i = c(1,3,4,4,8,9,11), j = c(7,2,4,5,3,10,9), val = c(10,8,3,1,1,2,20), compartment = c("AA","AA","AB","AB","BB","BB","AB"))
# create artificial TAD set in 20000 bp resolution
resolution <- 20000
tads <- data.frame(start = c(0,2,10) * resolution, end = c(2,8,13) * resolution, name = as.character(c(1,1,1)))
print(tads)
# convert basepairs to bins
tads$start <- tads$start / resolution
tads$end <- tads$end / resolution
print(tads)
# map interactions to TADs
interactions2tads(sparse.mtx, tads)
# map interactions to TADs and keep also compartment columns
interactions2tads(sparse.mtx, tads, cols = c("val","compartment"))

rz6/CopulaHiC documentation built on Dec. 31, 2019, 9:19 a.m.