Construct an interactome by comparing bait and control background across experimental conditions

Source: R/Main_functions.R

Construct an interactome by comparing bait and control background across experimental conditions

analyse_interactome(Intensity, Intensity_na_replaced = Intensity,
  conditions, bait_gene_name, Npep, Protein.IDs, names, bckg_bait,
  bckg_ctrl, by_conditions = TRUE, pool_background = TRUE,
  log_test = TRUE, log_stoichio = TRUE, substract_ctrl = TRUE,
  use_mean_for_bait = TRUE)

Arguments

Intensity

a data frame of protein intensities (without replacement of missing values). columns are experimental samples and rows are proteins
Intensity_na_replaced

a data frame of protein intensities (with replacement of missing values). columns are experimental samples and rows are proteins
conditions

: data frame describing the conditions corresponding to the columns of the data frame Intensity
bait_gene_name

: The gene name of the bait
Npep

: vector containing the number of theoretically observable peptide per protein (same length as dim(df)[1])
Protein.IDs

: vector containing protein IDs (same length as dim(df)[1])
names

: vector containing protein names (same length as dim(df)[1])
bckg_bait

: Name of the bait background as found in conditions$bckg
bckg_ctrl

: Name of the control background as found in conditions$bckg
by_conditions

option to perform the comparison between bait and control group for each condition
pool_background

option to use all control background conditions as one control group for all conditions
log_test

logical, perform t-test on log transform intensities
log_stoichio

logical, use the geometric mean instead of the arithmetic mean to compute stoichiometries
substract_ctrl

logical, substract ctrl intensities in the calculation of stoichiometries
use_mean_for_bait

logical, average bait intensities across all conditions to compute interaction stoichiometries

Value

an object of class InteRactome, i.e a list including the following elements :

conditions : a vector of experimental conditions.

names : a vector of names (by default gene names are used).

p_val : a list of vectors containing the p values associated to each experimental condition.

fold_change : a list of vectors containing the fold change associated to each experimental condition.

... : other variables.