performTest: Perform diffHic Test

In hicream: HI-C diffeREntial Analysis Method

Perform diffHic Test

Description

This function performs diffHic differential analysis for every pixel of the matrix.

Usage

performTest(
  matrices,
  cond,
  outFile = NULL,
  filterLc = FALSE,
  filterFlank = FALSE,
  flank = NULL
)

## S3 method for class 'resdiff'
print(x, ...)

## S3 method for class 'resdiff'
summary(object, ...)

## S3 method for class 'resdiff'
plot(x, whichPlot = c("p.value", "p.adj", "logFC"), ...)

Arguments

matrices	an object of class InteractionSet obtained from the function loadData. Conditions correspond to the columns (one column per replicate).
cond	a vector indicating the condition of each column of matrices.
outFile	path to export outputs of the function, set to NULL by default, in which case results are not exported.
filterLc	logical. Whether to filter out low counts or not. Set to FALSE by default, in which case no filtering is performed. See filterTrended for more details.
filterFlank	logical. Whether to filter out on enriched pairs. Set to FALSE by default, in which case no filtering is performed. See enrichedPairs and filterPeaks for more details.
flank	flank parameter used only if filterFlank = TRUE. Set to NULL by default. See enrichedPairs for more details.
x	a resdiff object to plot
...	not used
object	a resdiff object to print
whichPlot	a character string indicating which plot to display. Possible values are "p.value", "p.adj" and "logFC". Set to "p.value" by default.

Value

An object of class resdiff with the following entries:

region1	the first bin of the interaction
region2	the second bin of the interaction
p.value	the p-value of the diffHic test
p.adj	the adjusted p-value of the diffHic test
logFC	the log2-fold-change of the interaction

Author(s)

Élise Jorge [e-mail]
Sylvain Foissac [e-mail]
Pierre Neuvial [e-mail]
Nathalie Vialaneix [e-mail]

Examples

data("pighic")
resdiff <- performTest(pighic$data, pighic$conditions)
resdiff
summary(resdiff)
plot(resdiff)
plot(resdiff, whichPlot = "p.adj")
plot(resdiff, whichPlot = "logFC")

hicream documentation built on Aug. 8, 2025, 7:26 p.m.