ATA: Aggregate TAD analysis

In robinweide/GENOVA: GENOVA: expore the Hi-C

Aggregate TAD analysis

Description

Extracts Hi-C matrices around TADs, resizes these to a uniform size and averages the results for all TADs.

Usage

ATA(
  explist,
  bed,
  dist_thres = c(225000, Inf),
  size = 100L,
  outlier_filter = c(0, 1),
  anchors = NULL,
  raw = TRUE
)

Arguments

explist	Either a single GENOVA contacts object or a list of GENOVA contacts objects.
bed	A data.frame with in BED format, containing the a TAD region per row with the following three columns: A character giving the chromosome names. An integer with start positions. An integer with end positions.
dist_thres	An integer vector of length 2 indicating the minimum and maximum sizes of TADs to include in basepairs.
size	A code integer vector of length 1 noting the dimensions of the output.
outlier_filter	A numeric of length 2 between [0-1] indicating quantiles of data to be used as thresholds. Data outside these thresholds are set to the nearest threshold. Setting this to c(0, 1) performs no outlier correction.
anchors	(Optional) A matrix with two columns containing pre-computed anchor indices. If this is set, skips calculation of anchor indices and uses this argument instead. See anchors_ATA().
raw	A logical of length 1: should the raw array underlying the summary matrices be returned in the output? Should be TRUE if the intention is to use the quantify function.

Value

An ATA_discovery object containing the following slots:

signal

An array with the dimensions size x size x length(explist) containing mean bilinearly interpolated values across TADs.

signal_raw

A list with length(explist) elements for each contacts object, wherein an element is an n x size x size array with bilinearly interpolated contact values for each TAD. 'n' is the number of non-empty valid TADs.

Resolution recommendation

10kb-40kb

See Also

The rep_mat_lookup function that performs the lookup and summary for the ATA function and others.
The discovery class for a general description of discovery classes.
The visualise function for visualisation of the results.
The quantify function for quantification of TAD strenghts.
The anchors documentation for more information about anchors.

Other aggregate repeated matrix lookup analyses: APA(), ARA(), CSCAn(), PESCAn(), rep_mat_lookup()

robinweide/GENOVA documentation built on March 14, 2024, 11:16 p.m.