README.md

In rioualen/NetworkEval: What the Package Does (One Line, Title Case)

NetworkEval

The goal of NetworkEval is to evaluate the acccuracy of a set of interactions transcription factor-target gene in Escherichia coli K12, based on a set of custom control files.

Installation

remotes::install_github("rioualen/NetworkEval")

Example

The input interaction file must be formatted as follows:

• It is a tab-delimited file

• It has at least two columns containing TF bnumbers and target genes bnumbers, and named "tf_bnum" and "gene_bnum".

• Gene names can be converted to bnumbers using the EcoliGenes package (hopefully the conversion should be soon integrated in the evaluation process).

• Optionally, the file can contain one or more score columns, which name should be prefixed by "score_". This allows to generate ROC curves.

library(NetworkEval)

## Run a quick test set with small control sets || only works with a locally downloaded copy of the package - to be fixed
testfile="test_sets/test_90_10_scores.tsv"
run_eval(testfile, pos_set_id = "test_pos", neg_set_id = "test_neg")

## Run your own evaluation using all of the controls sets
run_eval("path/to/your/file")

rioualen/NetworkEval documentation built on April 10, 2021, 5:22 a.m.