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.
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")