match_IDs: Matching Gene IDs

In greenelab/ADAGEpath: ADAGE-based Signature Analysis

Matching Gene IDs

Description

Makes sure the input_data has the same gene IDs in the same order as the ADAGE model. It first converts gene IDs from the input_data to PAO1 locus tags. Then it re-orders input's rows according to gene order in ADAGE and fills in zero values for genes used in the ADAGE model but missed in the input_data.

Usage

match_IDs(input_data, ref_IDs)

Arguments

input_data	a data.frame containing geneIDs in the first column and each sample's gene expression values from the second column.
ref_IDs	a vector storing the reference geneIDs in the right order

Value

A data.frame containing the input_data's expression values after converting gene IDs, sorting gene orders, and filling in missing genes.

greenelab/ADAGEpath documentation built on May 25, 2022, 7:11 a.m.