InteractionCompare: FIREcaller: an R package for detecting frequently interacting...

In yycunc/FIREcaller: FIREcaller: an R package for detecting frequently interacting regions from Hi-C data

FIREcaller: an R package for detecting frequently interacting regions from Hi-C data

Description

Seperate function for calling differential FIREs outside of the main FIREcaller function

Usage

InteractionCompare(
  data,
  targetFile,
  coef = 2,
  adjust.method = "BH",
  adj.pvalue = 0.05,
  lfc = log2(2)
)

Arguments

data	a data frame of normalized cis-interactions, which are computed by FIREcaller, for each sample/replicate.
targetFile	a vector specifying the class of each sample/replicate.
coef	specifies the column number or column name for the interested coefficient or contrast of the linear model.
adjust.method	specifies the method used to adjust the p-values for multiple testing. Possible options include "none", "BH", "BY" and "holm". Default is adjust.method = "BH".
adj.pvalue	sets the cutoff value for adjusted p-values where only the interactions with lower adjusted p-values will be returned in the output.
lfc	sets the minimum absolute log2-fold-change required. Only the interactions with larger absolute log2-fold-change value are returned in the output.

yycunc/FIREcaller documentation built on Nov. 13, 2022, 7:49 p.m.