chromoR (version 1.0)

segmentCIM: Segments a 1D contact profile (1D CIM)

Description

This function finds changes points in a 1D Hi-C contact profile generated by taking the row sums of a pairwise chromosomal interactions map (CIM). It applies a wavelet change point algorithm [1] in order to find the location of change points (the segmentation of the profile).

Usage

segmentCIM(y, minL = 1, maxL = 1)

Arguments

y

A 1D Hi-C contact profile (a vector generated by taking row sums of a pairwise chromosomal interactions map (CIM)).

minL

Optional: a positive integer specifying the minimum level at which the search should be carried out. Set to 1 by default

maxL

Optional: a positive integer specifying the maximum level at which the search should be carried out and set to 1 by default. Should not exceed 0.1 of the length of the input. If the algorithm cannot find change points at the minimum level, it will repeat the search at higher levels and stop at the first level where change points were found or when it has reached the maximum level.

Value

Returns a list including the following objects:

changePoints

the location of change points (or NULL if none were found)

L

the level at which the change points were found (or the given maximal level if no change points were found)

Details

This function implemments a wavelet change point algorithm as described in [1] and based on its matlab implementation (http://homepages. ulb.ac.be/~majansen/software/index.html)

References

website: http://www.cl.cam.ac.uk/~ys388/chromoR/ (including more examples and data sets)

[1] M. Jansen, Chemometrics and intelligent laboratory systems, 2007, 85, 159.

See Also

See Also as compareCIM

Examples

data(imr90.1) # corrected contact map of imr90 (replicate 1) for chromosomes 1,2 
data(seg)
#generate a 1D profile for cis CIM of chromosome 2
indices = which(seg$chr == "chr2")
i1 = indices[1]
iN = indices[length(indices)]
p = rowSums(imr90.1[i1:iN, i1:iN]) - diag(imr90.1[i1:iN, i1:iN])
res = segmentCIM(p)
res