compute_amanida: Combine statistical results and compute vote-counting

In mariallr/amanida: Meta-Analysis for Non-Integral Data

Combine statistical results and compute vote-counting

Description

compute_amanida Combines for the same entry or metabolite the statistical values of p-value and fold-change. Also is computed a vote-counting for each compound. Compound combination is made with PubChem CID when is available.

Usage

compute_amanida(datafile, comp.inf = F)

Arguments

datafile	data imported using amanida_read function w/o names checked by check_names
comp.inf	include compounds IDs from PubChem, InChIKey, SMILES, KEGG, ChEBI, HMDB, Drugbank, Molecular Mass and Molecular Formula

Details

Entries corresponding to metabolites are combined as follows:

• P-values are combined using Fisher method weighted by N and gamma distribution

• Fold-change are combined by weighted mean. Transformation works with fold-change transformed to log scale with base 2.

Vote-counting is computed based on votes. Punctuation of entries is based on trend, up-regulation gives 1, down-regulation give -1 and equal behavior gives 0. Total sum is divided then by the total number of entries on each compound.

Value

METAtable S4 object with p-value combined, fold-change combined and vote-counting for each compound

Examples

## Not run: 
data("sample_data")

compute_amanida(sample_data)

## End(Not run)

mariallr/amanida documentation built on Jan. 30, 2024, 1:42 a.m.