identify_interactors: Identify specific interactors in an 'InteRactome'

In VoisinneG/InteRact: Analysis of affinity purification/tandem MS data

Identify specific interactors in an InteRactome

Description

Identify specific interactors in an InteRactome

Usage

identify_interactors(
  res,
  var_p_val = "p_val",
  p_val_thresh = 0.05,
  fold_change_thresh = 2,
  conditions = res$conditions,
  n_success_min = 1,
  consecutive_success = FALSE,
  p_val_breaks = c(1, min(1, 4 * p_val_thresh), min(1, 2 * p_val_thresh), min(1,
    p_val_thresh)),
  var_min_p_val = paste("min_", var_p_val, sep = ""),
  ...
)

Arguments

res	an InteRactome
var_p_val	name of the p-value variable
p_val_thresh	p-value threshold
fold_change_thresh	fold-change threshold
conditions	Select conditions used to identify interactors
n_success_min	minimal number of conditions in which the interactor must pass the the p-value and the fold-change thresholds
consecutive_success	logical, impose that the interactor must pass selection thresholds in n_success_min consecutive conditions.
p_val_breaks	numeric vector to discretize p-values. Passed to function order_interactome()
var_min_p_val	name of the p-value variable used to order the interactome. Passed to function order_interactome()
...	additionnal paramters passed to function order_interactome()

Value

an InteRactome with extra variables is_interactor, n_success and interactor

VoisinneG/InteRact documentation built on May 17, 2022, 11:40 p.m.