get_meta_data: Get Meta Data

In RGLab/HIPCMatrix: Microarray and RNA-seq Processing for ImmuneSpace

Get Meta Data

Description

Get meta data about how to process matrices within a study or how a matrix was processed.

Usage

get_meta_data(
  study,
  gef = NULL,
  fas_id = NULL,
  baseUrl = "https://datatools.immunespace.org"
)

Arguments

study	study accession
gef	gene expression files. Only required for SDY1529.
fas_id	Feature Annotation Set ID (from FeatureAnnotationSet table). If not provided, will attempt to derive based on study. Must be provided if study has not already been processed.
baseUrl	Base URL to pull feature annotation info from.

Details

Details such as file_location must be added manually to the meta_data_list object for new matrices. See internal Notion documentation for more details on how to update.

Value

List of meta data detailing how to process matrix. Includes:

file_location

Source for raw files. Options are gsm_soft: in data returned with GEOquery::getGEO(), gsm_supp_files: supplementary files in sample entry (GSM), gse_supp_files: supplementary files in experement entry (GSE), immport: raw files provided from ImmPort, custom: somewhere else (generally provided by immport as they wait for an update to make its way to GEO/ImmPort)

platform

Sequencing platform: Either Affymetrix, Illumina, Stanford (custom platform), or NA (RNA-seq). TODO: Add more descriptive identifier for RNA-seq

id_to_gse_mapping_info (optional)

Mapping info for data found in GSE to map ids to GSM (see source for more details)

custom_file_info (optional)

Details on where to find custom file for when file_location == "custom"

illumina_manifest_file (optional)

Path to manifest file for studies with Illumina idat files that need bgx manifest files.

gsm_table_var_name (optional)

Custom list of raw values column name for gsm-based data

RGLab/HIPCMatrix documentation built on Jan. 29, 2023, 5:13 a.m.