README.md

Brammer

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.

Install

To install the package, please execute the following command.

devtools::install_github("xilinshen/brammer")

Usage

Data preprocessing

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 ... CGGA_1002_B68.653.85107.130.220.760.250.054.1834.9433.29...100.92 6.1114.0651.530.060.0313.28163.330.005.18 CGGA_1003_B14.061.52 44.500.092.280.050.160.8651.14 4.62... 53.3727.50 4.2515.610.260.0812.16402.290.053.59 CGGA_1010_B 5.281.08 11.150.170.170.040.000.15 9.99 1.65... 4.91 9.21 4.92 1.210.000.07 0.61 0.430.000.66 CGGA_1014_B93.444.86 75.970.282.200.770.563.2444.3124.16...175.54 6.63 7.7222.210.160.0612.18172.120.054.13 CGGA_1017_B18.853.37 51.230.590.860.160.101.2614.9526.65... 28.76 9.5214.6417.090.080.05 5.73 98.530.001.18 CGGA_1018_B27.462.80 38.940.182.470.040.061.2854.6610.59... 63.3612.8117.6014.390.330.1012.74 73.550.065.03

Brain tumor subtyping

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 CGGA_1002_B0.9770.023C1 CGGA_1003_B0.7390.261C1 CGGA_1010_B1.0000.000C1 CGGA_1014_B0.2280.772C2 CGGA_1017_B0.9950.005C1 CGGA_1018_B0.9850.015C1

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.



xilinshen/brammer documentation built on Dec. 23, 2021, 6:21 p.m.