processDatasets: Processes JSON as a vector of datasets

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 vector of datasets

Description

Processes JSON as a vector of datasets

Usage

processDatasets(d)

Arguments

d	The JSON to process

Value

A data table with information about the queried dataset(s). A list if raw = TRUE. Returns an empty list if no datasets matched.

The fields of the output data.table are:

• experiment.shortName: Shortname given to the dataset within Gemma. Often corresponds to accession ID

• experiment.name: Full title of the dataset

• experiment.ID: Internal ID of the dataset.

• experiment.description: Description of the dataset

• experiment.troubled: Did an automatic process within gemma or a curator mark the dataset as "troubled"

• experiment.accession: Accession ID of the dataset in the external database it was taken from

• experiment.database: The name of the database where the dataset was taken from

• experiment.URI: URI of the original database

• experiment.sampleCount: Number of samples in the dataset

• experiment.batchEffectText: A text field describing whether the dataset has batch effects

• experiment.batchCorrected: Whether batch correction has been performed on the dataset.

• experiment.batchConfound: 0 if batch info isn't available, -1 if batch counfoud is detected, 1 if batch information is available and no batch confound found

• experiment.batchEffect: -1 if batch p value < 0.0001, 1 if batch p value > 0.1, 0 if otherwise and when there is no batch information is available or when the data is confounded with batches.

• experiment.rawData: -1 if no raw data available, 1 if raw data was available. When available, Gemma reprocesses raw data to get expression values and batches

• geeq.qScore: Data quality score given to the dataset by Gemma.

• geeq.sScore: Suitability score given to the dataset by Gemma. Refers to factors like batches, platforms and other aspects of experimental design

• taxon.name: Name of the species

• taxon.scientific: Scientific name for the taxon

• taxon.ID: Internal identifier given to the species by Gemma

• taxon.NCBI: NCBI ID of the taxon

• taxon.database.name: Underlying database used in Gemma for the taxon

• taxon.database.ID: ID of the underyling database used in Gemma for the taxon

PavlidisLab/gemma.R documentation built on April 16, 2024, 1:44 p.m.