Compute the FDR from the asymmetry of the volcano plot

Compute the FDR (False Discovery Rate) using the asymmetry of the volcano plot. It uses the fonction f(x) = c / (|x|-x0) with x = log10(fold_change), y=-log10(p_value) by default. Otherwise, custom x and y vectors can be provided. Points with x>x0 and y>f(x) are taken as true positive (TP) Points with x<x0 and y>f(x) are taken as false positive (FP) For a given set of parameters (c,x0), the FDR is given by TP/(TP+FP)

compute_FDR_from_asymmetry(df = NULL, x = NULL, y = NULL,
  c = seq(from = 0, to = 10, by = 0.1), x0 = seq(from = 0, to = 10, by
  = 0.1))

Arguments

df	: a data.frame containing columns p_val and fold_change
x	: numeric vector of x values. Only used if df is NULL.
y	: numeric vector of y values. Only used if df is NULL.
c	: numeric vector
x0	: numeric vector

Value

a data.frame with a extra column FDR if df is not NULL. A vector of FDR values otherwise.

If parameters c and x0 are vectors, FDR is taken as the minimum FDR value across all sets of parameters

Examples

#' #load data :
data("proteinGroups_Cbl")
#Run InteRact with default parameters
res <- InteRact(proteinGroups_Cbl, bait_gene_name = "Cbl")
#> Warning: Column 'Score' not available : Data NOT Filtered based on portein identification score
#> Contaminant proteins discarded
#> Proteins with no gene name available discarded
#> Number of theoretically observable peptides unavailable : used MW instead
#> Merge protein groups associated to the same gene name (sum of intensities) 
#> Rescale median intensity across conditions
#> Replace missing values and perform interactome analysis for 1 replicates
#> Nrep=1
#> Averaging 1 interactomes
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
#> Warning: NaNs produced
df_merge <- merge_conditions(res)
df_FDR <- compute_FDR_from_asymmetry(df_merge)
#> Compute FDR...
#> 
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Interactome <- append_FDR(res, cbind(df_merge, FDR = df_FDR$FDR) )