Based on expression profiles, this Brammer applification could subtyping brain tumor patients with different immune infiltration signatures (i.e. C1/2 subtypes). The C1 subtype enriches for a constellation of protective markers for prognosis, such as high infiltration of CD8+ T cells and nature killer cells. The C2 subtype has an extensive infiltration of tumor-associated macrophages and microglia, and was enriched with immune suppressive, wound healing and angiogenic signatures.
To install the package, please execute the following command.
devtools::install_github("xilinshen/brammer")
The gene expression should be normalized as CPM values. Please make sure each row of expression matrix represent a patient and each column represent a Hugo Symbol of human gene.
Here's an example :
load(system.file("data/CGGA_toydata.rda",package = "brammer"))
head(data)
A data.frame: 6 × 23987
A1BGA1BG.AS1A2MA2M.AS1A2ML1A2MP1A3GALT2A4GALTAAASAACS...ZYXZZEF1ZZZ3hsa.mir.1199hsa.mir.125ahsa.mir.335hsa.mir.6080hsa.mir.6723hsa.mir.7162hsa.mir.8072
Brammer could classifies patients into C1/2 subtypes through expression matrix of brain tumor.
subtyping_result = brammer::model_predict(data)
head(subtyping_result)
A data.frame: 6 × 3
C1 probability (%)C2 probability (%)subtype
The columns "C1 probability (%)" and "C2 probability (%)" represent the probability that the patients belongs to C1/2 subtypes, respectively. The column "subtype" represent brain tumor subtypes of patients predict by brammer.
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