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

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.

1 | ```
compareCIM(m1, m2, seg, bfThreshold = 6.1)
``` |

`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). |

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 |

Yoli Shavit

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

See Also `segmentCIM`

1 2 3 4 5 6 7 | ```
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
``` |

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

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