assessComplexFeaturesWithSEC: Check for each feature in 'detected.features' if there is...

In hafenr/MACode: Functions and code snippets for my master thesis

Description

Check for each feature in 'detected.features' if there is another feature in 'true.positive.features' that is close to it. The endresult is a DF of feature retention times that are flagged with either 'FP', 'TP', 'TN', or 'FN'.

Usage

assessComplexFeaturesWithSEC(true.positive.features, detected.features,
  all.complexes, min.rt, max.rt, feature.vicinity.tol = 5)

Arguments

true.positive.features	data.table of true, manually annotated features. The DF must have the columns: 'complex_id', 'rt'.
detected.features	data.table of detected features. The DF must have the columns: 'complex_id', 'center_rt'.
all.complexes	A list of unique complex ids that should be checked for features. Every SEC position for each of those complexes will be checked for a detected feature.
feature.vicinity.tol	A number that indicates how close an experimentally determined feature has to be to a manually annotated one, to still count as a true positive. experimentally determined feature has to be to a manually annotated one, to still count as a true positive.

Value

A data.table with the columns: 'complex_id', 'rt', 'type', where type is of type character an is either 'FP', 'FN', 'TP', 'TN'.

Examples

manual.annotations.raw <- readManualAnnotationFile(annotations.1.raw)
manual.annotations <-
    createManualComplexAnnotations(
     manual.annotations.1.raw, 'apexes_partially_observed')
detected.features <- fread('cprophet_output/sec_complexes.tsv')
assessed.feats <-
    assessComplexFeaturesWithSEC(manual.annotations,
                                 detected.features, all.complexes)

hafenr/MACode documentation built on May 17, 2019, 2:24 p.m.