SVM (support vector machine)

Input

Two datasets, one for training and one for testing

Example training dataset:

id	S01	S02	S03	S04	S05	S06	S07	S08	S09	S10	S11	S12	S13	S14	S15	S16	S17	S18	S19	S20	S21	S22	S23	S24	S25	S26	S27	S28	S29	S30	S31	S32	S33	S34	S35	S36	S37	S38
class	Type_L	Type_L	Type_L	Type_L	Type_CL	Type_L	Type_L	Type_L	Type_L	Type_B	Type_CL	Type_L	Type_L	Type_B	Type_B	Type_B	Type_B	Type_L	Type_B	Type_B	Type_B	Type_L	Type_N	Type_N	Type_N	Type_L	Type_L	Type_L	Type_CL	Type_L	Type_L	Type_B	Type_L	Type_CL	Type_B	Type_L	Type_B	Type_L
ENSG00000000419	5.32	5.3	6.64	5.6	6.61	5.24	6.66	6.62	6.41	5.19	6.16	7.29	4.78	6.14	5.66	5.8	6.2	4.69	6.5	5.49	7.29	5.23	5.63	4.82	5.64	6.07	4.79	6.25	5.19	5.8	4.63	5.98	6.19	4.97	4.15	5.82	6.4	4.67
ENSG00000001036	6.11	4.8	4.47	4.99	6.94	5	5.11	5.42	4.58	4.74	6.03	5.47	4.32	6.16	5.89	5.37	6.01	4.72	5.17	5.96	6.35	5.02	5.31	6.37	5.24	6.29	5.81	4.16	6.56	5.91	5.19	4	5.48	4.14	5.9	5.51	5.14	6.22
ENSG00000001084	5.78	4.01	5.14	5.11	3.63	5.93	4.11	3.68	3.23	5.01	5.81	4.5	5.17	5.61	6.19	5.02	6.79	5.97	4.77	5.85	4.78	4.27	6.8	6.25	4.5	5.08	5.21	4.24	4.12	6	4.16	3.19	4.29	3.95	5.26	6.63	4.38	6.38
…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…	…

Example testing dataset:

id	T01	T02	T03	T04	T05	T06	T07	T08	T09	T10	T11	T12	T13	T14
ENSG00000000419	6.06	5.25	5.15	5.36	5.22	5.75	4.79	6.01	6.39	7.71	5.7	5.85	5.34	5.07
ENSG00000001036	4.47	5.39	5.28	5.82	5.75	6.96	6.09	5.07	5.3	5.76	5.4	4.27	5.03	5.68
ENSG00000001084	4.47	6	5.77	5.76	5.76	4.64	4.07	4.52	4.16	3.24	4.35	2.49	5.89	4.37
ENSG00000001497	5.27	4.27	6.58	5.54	5.57	6.4	4.91	4.79	4.95	5.83	4.89	5.33	4.23	6.03
…	…	…	…	…	…	…	…	…	…	…	…	…	…	…

Code

R Code to run SVM

Output

Prediction_test

Sample	Class
T01	Type_N
T02	Type_N
T03	Type_B
T04	Type_B
T05	Type_B
T06	Type_CL
T07	Type_CL
T08	Type_L
T09	Type_L
T10	Type_L
T11	Type_L
T12	Type_L
T13	Type_L
T14	Type_L

Predict_stat

Overall accuracy for the training set: 0.8684211 Confusion matrix:

True predicted	Type_B	Type_CL	Type_L	Type_N
Type_B	11	0	0	0
Type_CL	0	4	0	0
Type_L	1	0	20	0
Type_N	1	0	0	3