TB_indian: An example TB dataset with Indian population data.

In compbiomed/TBSignatureProfiler: Profile RNA-Seq Data Using TB Pathway Signatures

An example TB dataset with Indian population data.

Description

An example dataset containing the gene expression and metadata in a SummarizedExperiment object for an Indian population. Active TB contamination of the 44 subjects is denoted for each as a "1"(active) or "0" (latent/not present), and can be accessed via TB_indian$label. The SummarizedExperiment object contains 2 assays (counts and log(counts)), and the column names give the unique subject identification number along with the subject's gender.

Usage

TB_indian

Format

SummarizedExperiment

Details

This dataset was published as part of a study to assess performance of published TB signatures in a South Indian population (Leong et. al 2018). RNA sequencing was performed on whole blood PAX gene samples collected from 28 TB patients and 16 latent TB infected (LTBI) subjects enrolled as part of an ongoing household contact study. Whole blood RNA-Seq analysis was performed on all 44 participants.

References

Leong S., Zhao Y., et. al. (2018). Existing blood transcriptional classifiers accurately discriminate active tuberculosis from latent infection in individuals from south India. Tuberculosis 109, 41-51. doi: 10.1016/j.tube.2018.01.002.

Examples

data("TB_indian")

compbiomed/TBSignatureProfiler documentation built on April 9, 2024, 10:46 p.m.