hicream (version 0.0.4)

performTest: 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 resdiff
print(x, ...)
# S3 method for resdiff
summary(object, ...)
# S3 method for resdiff
plot(x, whichPlot = c("p.value", "p.adj", "logFC"), ...)

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

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.

Author

Élise Jorge
Sylvain Foissac
Toby Dylan Hocking
Pierre Neuvial
Nathalie Vialaneix

Examples

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