processDEA: Processes JSON as a differential expression analysis

In PavlidisLab/gemma.R: A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

Processes JSON as a differential expression analysis

Description

Processes JSON as a differential expression analysis

Usage

processDEA(d)

Arguments

d	The JSON to process

Value

A data table with information about the differential expression analysis of the queried dataset. Note that this funciton does not return differential expression values themselves. Use get_differential_expression_values to get differential expression values (see examples).

The fields of the output data.table are:

• result.ID: Result set ID of the differential expression analysis. May represent multiple factors in a single model.

• contrast.ID: Id of the specific contrast factor. Together with the result.ID they uniquely represent a given contrast.

• experiment.ID: Id of the source experiment

• factor.category: Category for the contrast

• factor.category.URI: URI for the contrast category

• factor.ID: ID of the factor

• baseline.factors: Characteristics of the baseline. This field is a data.table

• experimental.factors: Characteristics of the experimental group. This field is a data.table

• isSubset: TRUE if the result set belong to a subset, FALSE if not. Subsets are created when performing differential expression to avoid unhelpful comparisons.

• subsetFactor: Characteristics of the subset. This field is a data.table

• probes.analyzed: Number of probesets represented in the contrast

• genes.analyzed: Number of genes represented in the contrast

PavlidisLab/gemma.R documentation built on Oct. 25, 2024, 10:59 a.m.