compareCIM: Compares 2 CIMs

In chromoR: Analysis of chromosomal interactions data (correction, segmentation and comparison)

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

Author(s)

Yoli Shavit

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

Example output

Loading required package: haarfisz
Loading required package: wavethresh
Loading required package: MASS
WaveThresh: R wavelet software, release 4.6.8, installed

Copyright Guy Nason and others 1993-2016

Note: nlevels has been renamed to nlevelsWT

Loading required package: gdata
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to locate valid perl interpreter
gdata: 
gdata: read.xls() will be unable to read Excel XLS and XLSX files
gdata: unless the 'perl=' argument is used to specify the location of a
gdata: valid perl intrpreter.
gdata: 
gdata: (To avoid display of this message in the future, please ensure
gdata: perl is installed and available on the executable search path.)
sh: 1: cannot create /dev/null: Permission denied
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLX' (Excel 97-2004) files.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: 'gdata'

The following object is masked from 'package:stats':

    nobs

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data frame with 0 columns and 0 rows

chromoR documentation built on May 2, 2019, 2:05 p.m.