PESCAn: Paired-end spatial chromatin analysis
In robinweide/GENOVA: GENOVA: expore the Hi-C

PESCAn

R Documentation

Paired-end spatial chromatin analysis

Description

Performs an all-to-all Hi-C contact analysis for specified regions.

Usage

PESCAn(
  explist,
  bed,
  shift = 1000000L,
  dist_thres = c(5000000L, Inf),
  size_bin = NULL,
  size_bp = NULL,
  outlier_filter = c(0, 1),
  min_compare = 10,
  anchors = NULL,
  raw = TRUE
)

Arguments

`explist`	Either a single GENOVA `contacts` object or a list of GENOVA `contacts` objects.
`bed`	A BED-formatted `data.frame` with the following 3 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_PESCAn()`.
`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 PESCAn_discovery object containing the following slots:

obsexp: An array with the dimensions size_bin x size_bin 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 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 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.

Resolution recommendation

20kb-40kb

Examples

## Not run: 
# Typical usage: PESCAn for super enhancers using a 1 MB
# circular permutation on a pair of experiments.
pescan <- PESCAn(
  explist = list(WT_40kb, KO_40kb),
  bed = super_enhancers,
  shift = 1e6
)

# Alternative usage with pre-calculated anchors and no permutation
anchors <- anchors_PESCAn(WT_40kb$IDX, resolution(WT_40kb),
  genes_tss,
  dist_thres = c(5e6, 15e6)
)
pescan <- PESCAn(
  explist = list(WT_40kb),
  anchors = anchors,
  shift = 0
)

# Visualising PE-SCAns
visualise(pescan)

## End(Not run)

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