get_dataset_differential_expression_analyses: Retrieve annotations and surface level stats for a dataset's...

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

Retrieve annotations and surface level stats for a dataset's differential analyses

Description

Retrieve annotations and surface level stats for a dataset's differential analyses

Usage

get_dataset_differential_expression_analyses(
  dataset,
  raw = getOption("gemma.raw", FALSE),
  memoised = getOption("gemma.memoised", FALSE),
  file = getOption("gemma.file", NA_character_),
  overwrite = getOption("gemma.overwrite", FALSE)
)

Arguments

dataset	A numerical dataset identifier or a dataset short name
raw	TRUE to receive results as-is from Gemma, or FALSE to enable parsing. Raw results usually contain additional fields and flags that are omitted in the parsed results.
memoised	Whether or not to save to cache for future calls with the same inputs and use the result saved in cache if a result is already saved. Doing options(gemma.memoised = TRUE) will ensure that the cache is always used. Use forget_gemma_memoised to clear the cache.
file	The name of a file to save the results to, or NULL to not write results to a file. If raw == TRUE, the output will be the raw endpoint from the API, likely a JSON or a gzip file. Otherwise, it will be a RDS file.
overwrite	Whether or not to overwrite if a file exists at the specified filename.

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

Examples

result <- get_dataset_differential_expression_analyses("GSE2872")
get_differential_expression_values(resultSet = result$result.ID[1])

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