correctPairCIM: Corrects a pairwise CIM

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/VarianceStabCorrection.R

Description

This function applies a wavelet based correction to remove bias and noise, typical of Hi-C data, from pairwise chromosomal interaction maps(CIM).

Usage

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correctPairCIM(m, isCis)

Arguments

m

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.

isCis

A boolean specifying whether this matrix describes cis (the same chromosome) or trans (different chromosomes) pairwise contacts.

Value

Returns the corrected CIM

Author(s)

Yoli Shavit

References

http://www.cl.cam.ac.uk/~ys388/chromoR/

See Also

See Also correctCIM, compareCIM

Examples

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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$chr == "chr1")
i1 = indices[1]
iN = indices[length(indices)]
indices = which(seg.imr90.obs$chr == "chr2")
j1 = indices[1]
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

chromoR documentation built on May 30, 2017, 5:08 a.m.