subset_curatedTBData: Subset curatedTBData based on single/multiple conditions

In compbiomed/curatedTBData: Curation of existing tuberculosis transcriptomic studies

Subset curatedTBData based on single/multiple conditions

Description

The function selects desired samples from curatedTBData database based pre-specified conditions

Usage

subset_curatedTBData(
  theObject,
  annotationColName,
  annotationCondition,
  assayName = NULL
)

Arguments

theObject	A SummarizedExperiment or MultiAssayExperiment object.
annotationColName	A character indicates feature of interest in the object's annotation data.
annotationCondition	A vector of character indicates conditions want to be selected.
assayName	A character indicates the name of the assay from the input object. The default is NULL. When assayName is NULL, the function selects the first assay along assay list.

Value

A SummarizedExperiment object containing subjects with desired annotation conditions.

Examples

obj <-  curatedTBData("GSE74092", dry.run = FALSE, curated.only = TRUE)
subset_curatedTBData(obj[[1]], annotationColName = "TBStatus",
                     annotationCondition = c("Control","PTB"))

compbiomed/curatedTBData documentation built on March 14, 2024, 2:08 p.m.