CSCAn: Cross spatial chromatin analysis
In robinweide/GENOVA: GENOVA: expore the Hi-C

CSCAn

R Documentation

Cross spatial chromatin analysis

Description

Takes a list of BED-like genomic locations and makes a Hi-C contact analysis for crosswise pairs between elements of that list.

Usage

CSCAn(
  explist,
  bedlist,
  shift = 1000000L,
  dist_thres = c(NA, 1e+06),
  size_bin = NULL,
  size_bp = NULL,
  outlier_filter = c(0, 1),
  min_compare = 10,
  anchors = NULL,
  raw = TRUE,
  group_direction = FALSE
)

Arguments

`explist`	Either a single GENOVA `contacts` object or a list of GENOVA `contacts` objects.
`bedlist`	A named `list` of length >= 2 wherein each element is a BED-like `data.frame` with the following three columns: A `character` giving the chromosome names. An `integer` with start positions. An `integer` with end positions.
`shift`	An `integer` of length 1 indicating how many basepairs the anchors should be shifted. Essentially performs circular permutation of `size` for a reasonable estimate of background. The argument is ignored when `shift <= 0`.
`dist_thres`	An `integer` vector of length 2 indicating the minimum and maximum distances in basepairs between anchorpoints.
`size_bin`, `size_bp`	The size of the lookup regions in bins (i.e. a score of 21 yields an output with 10 Hi-C bins both up- and downstream of the anchor). When `NULL` (default), it is internally set to `21` when the `size_bp` is also `NULL`. `size_bp` is an alternative parametrisation for the lookup regions, expressed in basepairs. `size_bp` is not used when the argument `size_bin` is set.
`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.
`min_compare`	An `integer` of length 1 indicating the minimum number of pairwise interactions on a chromosome to consider.
`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_CSCAn()`.
`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.
`group_direction`	A `logical` of length 1 which when `TRUE` will mirror groups for anchors, where the left anchor location is larger than the right anchor location. Left and right refer to the `bedlist` elements that generate combinations.

Value

An CSCAn_discovery object containing the following slots, wherein i is the number of combinations between the bedlist argument elements:

obsexp: An array with the dimensions size_bin x size_bin x i x length(explist) containing fold change values for the signal over the median shifted values.
signal: An array with the dimensions size_bin x size_bin x i x length(explist) containing mean contact values for bins surrounding the anchors.
signal_raw: A list with length(explist) elements for each contacts object, wherein an element is an n x size_bin x size_bin array with contact values for each anchor. 'n' is the number of non-empty valid anchors.
shifted: An array with the dimensions size_bin x size_bin x i x length(explist) containing mean contact values for bins that are shift basepairs away from the anchors.
shifted_raw: A list with length(explist) elements for each contacts object, wherein an alemeent is an n x size_bin x size_bin array with contact values for each shifted anchors. 'n' is the number of non-empty valid (unshifted) anchors.

Examples

## Not run: 
cscan <- CSCAn(list(WT_20kb, KO_20kb),
               bedlist = list(group_A, group_B))
               
visualise(cscan)

## End(Not run)

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