postHoc: Perform Post Hoc Inference

In hicream: HI-C diffeREntial Analysis Method

Perform Post Hoc Inference

Description

This function performs post-hoc inference on all provided clusters using performTest results.

Usage

postHoc(resdiff, clusters, alpha)

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

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

## S3 method for class 'resposthoc'
plot(x, ...)

Arguments

resdiff	An object of class resdiff obtained from the function performTest.
clusters	A vector corresponding to a clustering of resdiff rows.
alpha	A number between 0 and 1 at which the computed post hoc bounds will be valid.
x	a resposthoc object to plot
...	not used
object	a resposthoc object to summarize

Value

An object of class resposthoc containing a matrix with true positive proportions for each interaction and a dataframe with the following entries:

region1	The first bin of the interaction.
region2	The second bin of the interaction.
clust	The cluster the interaction belongs to.
TPRate	The minimal post hoc true positive proportion of the cluster the interaction belongs to.
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.
meanlogFC	The mean of the log2-fold-change for the cluster the interaction belongs to.
varlogFC	The variance of the log2-fold-change for the cluster the interaction belongs to.
propPoslogFC	The proportion of interactions with positive log2-fold-change in the cluster the interaction belongs to.

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)
res2D <- AggloClust2D(pighic$data)
if (!is.null(res2D)) { # in case Python or modules are not available
  clusters <- res2D$clustering
  alpha <- 0.05
  resposthoc <- postHoc(resdiff, clusters, alpha)
  resposthoc
  summary(resposthoc)
  plot(resposthoc)
}

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