calculate_precision: Calculate precision at each point in a sequence

In PrInCE: Predicting Interactomes from Co-Elution

Description

Calculate the precision of a list of interactions at each point in the list, given a set of labels.

Usage

calculate_precision(labels)

Arguments

labels

a vector of zeroes (FPs) and ones (TPs)

Value

a vector of the same length giving the precision at each point in the input vector

Examples

## calculate features
data(scott)
data(scott_gaussians)
subset <- scott[seq_len(500), ] ## limit to first 500 proteins
gauss <- scott_gaussians[names(scott_gaussians) %in% rownames(subset)]
features <- calculate_features(subset, gauss)
## make training labels
data(gold_standard)
ref <- adjacency_matrix_from_list(gold_standard)
labels <- make_labels(ref, features)
## predict interactions with naive Bayes classifier
ppi <- predict_ensemble(features, labels, classifier = "NB", cv_folds = 3, 
                        models = 1)
## tag precision of each interaction
ppi$precision <- calculate_precision(ppi$label)

PrInCE documentation built on Nov. 8, 2020, 6:34 p.m.