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

	A1BG	A1BG.AS1	A2M	A2M.AS1	A2ML1	A2MP1	A3GALT2	A4GALT	AAAS	AACS	...	ZYX	ZZEF1	ZZZ3	hsa.mir.1199	hsa.mir.125a	hsa.mir.335	hsa.mir.6080	hsa.mir.6723	hsa.mir.7162	hsa.mir.8072
	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	...	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>	<dbl>
CGGA_1002_B	68.65	3.85	107.13	0.22	0.76	0.25	0.05	4.18	34.94	33.29	...	100.92	6.11	14.06	51.53	0.06	0.03	13.28	163.33	0.00	5.18
CGGA_1003_B	14.06	1.52	44.50	0.09	2.28	0.05	0.16	0.86	51.14	4.62	...	53.37	27.50	4.25	15.61	0.26	0.08	12.16	402.29	0.05	3.59
CGGA_1010_B	5.28	1.08	11.15	0.17	0.17	0.04	0.00	0.15	9.99	1.65	...	4.91	9.21	4.92	1.21	0.00	0.07	0.61	0.43	0.00	0.66
CGGA_1014_B	93.44	4.86	75.97	0.28	2.20	0.77	0.56	3.24	44.31	24.16	...	175.54	6.63	7.72	22.21	0.16	0.06	12.18	172.12	0.05	4.13
CGGA_1017_B	18.85	3.37	51.23	0.59	0.86	0.16	0.10	1.26	14.95	26.65	...	28.76	9.52	14.64	17.09	0.08	0.05	5.73	98.53	0.00	1.18
CGGA_1018_B	27.46	2.80	38.94	0.18	2.47	0.04	0.06	1.28	54.66	10.59	...	63.36	12.81	17.60	14.39	0.33	0.10	12.74	73.55	0.06	5.03

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
	<dbl>	<dbl>	<chr>
CGGA_1002_B	0.977	0.023	C1
CGGA_1003_B	0.739	0.261	C1
CGGA_1010_B	1.000	0.000	C1
CGGA_1014_B	0.228	0.772	C2
CGGA_1017_B	0.995	0.005	C1
CGGA_1018_B	0.985	0.015	C1

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.