TB_hiv: An example TB dataset with TB/HIV data.

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

An example TB dataset with TB/HIV data.

Description

An example dataset containing the gene expression and metadata in a SummarizedExperiment object for 31 subjects with HIV and/or Tuberculosis diseases. Information on subject infection status can be accessed with TB_hiv$Disease. Samples with both TB and HIV contamination are marked as tb_hiv, while samples with HIV and no TB are marked as hiv_only.

Usage

TB_hiv

Format

SummarizedExperiment

Details

This dataset was published as part of a study to assess whether gene expression signatures and cytokine levels would distinguish active TB in advanced HIV in a cohort residing in Sub-Saharan Africa (Verma et. al 2018). Participants were severely immunosuppressed TB-HIV patients who had not yet received TB treatment or anti-retroviral therapy (ART). The dataset included in this package has been lightly edited from the originally published dataset due to the removal of one participant who was HIV positive, on ART and developed TB during follow-up. Whole blood RNA-Seq analysis was performed on all 31 participants.

References

Verma S., Du P., et. al. (2018). Tuberculosis in advanced HIV infection is associated with increased expression of IFN and its downstream targets. BMC Infectious Diseases 18:220. doi: https://doi.org/10.1186/s12879-018-3127-410.1186/s12879-018-3127-4.

Examples

data("TB_hiv")

compbiomed/TBSignatureProfiler documentation built on Oct. 29, 2024, 6:07 a.m.