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

View source: R/domainDirections.R

Collect directionality statistics for domain identification with genomic bins.

1 | ```
domainDirections(files, param, width=50000, span=10)
``` |

`files` |
a character vector containing paths to the index files generated from each Hi-C library |

`param` |
a |

`width` |
an integer scalar specifying the width of each bin in base pairs |

`span` |
an integer scalar specifying the distance to consider for up/downstream interactions |

The genome is partitioned into bins of size `width`

.
For each bin, this function computes the total number of read pairs between that bin and the `span`

upstream bins (i.e., those with higher genomic coordinates).
This is repeated for the `span`

downstream bins, thus yielding two counts (up and down) per bin.

A RangedSummarizedExperiment is returned containing the coordinates of each bin and two matrices of counts, named `"up"`

and `"down"`

.
Each row of the matrix corresponds to a bin, while each column corresponds to a library in `files`

.
Each entry of the matrix stores the total count of read pairs to upstream or downstream bins.

The total up- and downstream counts can be used to compute a directionality statistic, e.g., as defined by Dixon et al, or by computing the log-fold change between fields. Alternatively, it can be used to identify differential domains - see the user's guide for more details.

A RangedSummarizedExperiment object with one row for each bin in the genome.
It contains two integer matrices named `"up"`

and `"down"`

, containing the counts to upstream and downstream bins respectively.

Aaron Lun

Dixon JR et al. (2012). Topological domains in mammalian genomes identified by analysis of chromatin interactions. *Nature* 485:376-380.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | ```
hic.file <- system.file("exdata", "hic_sort.bam", package="diffHic")
cuts <- readRDS(system.file("exdata", "cuts.rds", package="diffHic"))
param <- pairParam(fragments=cuts)
# Setting up the parameters
fout <- tempfile(fileext=".h5")
invisible(preparePairs(hic.file, param, file=fout))
# Not really that informative; see user's guide.
out <- domainDirections(fout, param, width=10)
out
# Calculating directionality log-FC with a large prior.
up.counts <- assay(out, "up")
down.counts <- assay(out, "down")
dir.logFC <- log2((up.counts+10)/(down.counts+10))
dir.logFC
# Calculating directionality index with Dixon's method.
dixon.stat <- sign(up.counts-down.counts)*2*(
(up.counts-down.counts)/(up.counts+down.counts))^2
dixon.stat
``` |

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