This function applies a wavelet based correction to remove bias and noise, typical of Hi-C data, from pairwise chromosomal interaction maps(CIM).
A pairwise (i.e between 2 chromosomes) CIM (matrix), where the cell m[i,j] is the interaction frequency between the genomic region i and the genomic region j.
A boolean specifying whether this matrix describes cis (the same chromosome) or trans (different chromosomes) pairwise contacts.
Returns the corrected CIM
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# correction of a single pair data(imr90.1.obs) data(seg.imr90.obs) # take a pairwise matrix and correct it indices = which(seg.imr90.obs$chr == "chr1") i1 = indices iN = indices[length(indices)] indices = which(seg.imr90.obs$chr == "chr2") j1 = indices jN = indices[length(indices)] m.1.2 = imr90.1.obs[i1:iN, j1:jN] # set isCis to FALSE because we correct for a pair of different chromosomes m.1.2.corrected = correctPairCIM(m.1.2, FALSE) m.1.2.corrected
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