callInteractions: Call significant interactions

In Pasquali-lab/UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

Call significant interactions

Description

Test a set of query_regions for significant interactions with the viewpoint.

Usage

callInteractions(
  umi4c,
  design = ~condition,
  query_regions,
  padj_method = "fdr",
  zscore_threshold = 2,
  padj_threshold = 0.1,
  alpha = 20,
  penalty = 0.1
)

Arguments

umi4c	UMI4C object as generated by makeUMI4C or the UMI4C constructor.
design	A formula or matrix. The formula expresses how the counts for each fragment end depend on the variables in colData. See DESeqDataSet.
query_regions	GRanges object or data.frame containing the coordinates of the genomic regions you want to use to perform the analysis in specific genomic intervals. Default: NULL.
padj_method	The method to use for adjusting p-values, see p.adjust. Default: fdr.
zscore_threshold	Numeric indicating the z-score threshold to use to define significant differential contacts. Default: 2.
padj_threshold	Numeric indicating the adjusted p-value threshold to use to define significant differential contacts. Default: 0.1.
alpha	Approximate number of fragments desired for every basis function of the B-spline basis. floor((max(number of fragments)) / alpha) is passed to create.bspline.basis as nbasis argument. 4 is the minimum allowed value. Default: 20.
penalty	Amount of smoothing to be applied to the estimated functional parameter. Default: 0.1.

Value

GRangesList where each element is a UMI4C sample with the queried regions and their adjusted p-values and Z-scores.

Examples

data("ex_ciita_umi4c")
umi <- ex_ciita_umi4c
win_frags <- makeWindowFragments(umi, n_frags=8, sliding=1)

gr <- callInteractions(umi, ~condition, win_frags, padj_threshold = 0.01, zscore_threshold=2)
inter <- getSignInteractions(gr)

Pasquali-lab/UMI4Cats documentation built on March 23, 2024, 9:42 p.m.