chromoR (version 1.0)

compareCIM: Compares 2 CIMs

Description

Finds regions pairs that present significantly different interaction frequency between 2 chromosomal interactions maps (CIMs). Specifically, a Bayes Factor (BF) term is calculated for each pair and pairs with a BF score above a given threshold are reported.

Usage

compareCIM(m1, m2, seg, bfThreshold = 6.1)

Arguments

m1

The first CIM (matrix) to be compared, where the cell m[i,j] is the interaction frequency between the genomic region i and the genomic region j.

m2

The second CIM (matrix) to be compared, where the cell m[i,j] is the interaction frequency between the genomic region i and the genomic region j. (m1 and m2 should be of the same dimensions)

seg

A data table definding a genome segmentation, giving the genomic coordinates of each row/col in the given CIM. The data table should include the following columns for each region: chromosome name, start position and end position. Users may also provide additional properties in the the next columns such as gene expression or cytogenetic band.

bfThreshold

Optional: the Bayes Factor cuttoff (set to 6.1 by default).

Value

Returns a list with the following objects:

sigChanges

a data table listing all significant changes: the corrdinates of each region, the Bayes Factor value, the original and standartized values of the region pair in m1 and m2

mBf

the Bayes Factor matrix giving the Bayes Factor value for each regions pair

References

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

See Also

See Also segmentCIM

Examples

data(imr90.1) # corrected contact map of imr90 (replicate 1) for chromosomes 1,2 
data(imr90.2) # corrected contact map of imr90 (replicate 2) for chromosomes 1,2 
data(seg)
# compare replicates of the same celll type
res = compareCIM(imr90.1, imr90.2, seg) 
# no significant changes identified
res$sigChanges