使用方法：
usage: /share/nas1/huangls/test/TCGA_GEO_immu/scripts/subset_column.r
[-h] -i input -m idlist [-c colname] [-o outdir] [-p prefix]
get data by column ID
optional arguments:
-h, --help show this help message and exit
-i input, --input input
input matrix data [required]
-m idlist, --idlist idlist
input column ID list ,default first column [required]
-c colname, --colname colname
match column name in idlist [required]
-o outdir, --outdir outdir
output file directory [default cwd]
-p prefix, --prefix prefix
output file name prefix [default demo]
参数说明：
-i 输入要处理的表格，第一列会都成行名
|
TCGA-D7-A74A-01A-11R-A32D-31 |
TCGA-BR-7704-01A-11R-2055-13 |
TCGA-VQ-A91N-01A-11R-A414-31 |
TCGA-CD-A4MH-01A-11R-A251-31 |
| TSPAN6 |
19.71229 |
15.16812 |
58.95336274 |
112.4479129 |
| TNMD |
0.128679 |
0 |
0 |
0.417115888 |
| DPM1 |
166.1934 |
229.3096 |
160.0258308 |
223.6269896 |
| SCYL3 |
8.721258 |
3.71577 |
18.44681977 |
8.307169238 |
| C1orf112 |
6.935284 |
2.181263 |
16.46792983 |
7.387781561 |
| FGR |
2.251234 |
18.9202 |
3.145843585 |
7.801411858 |
| CFH |
3.535552 |
14.03032 |
12.53080064 |
10.27682391 |
| FUCA2 |
103.1044 |
119.298 |
128.6210801 |
138.7011133 |
| GCLC |
30.47744 |
25.12227 |
30.24963988 |
25.52302692 |
-m 指定ID列表，-c colname 指定哪一列作为ID列表的列表；
| barcode |
patient |
shortLetterCode |
definition |
stage |
| TCGA-B7-A5TK-01A-12R-A36D-31 |
TCGA-B7-A5TK |
TP |
Primary solid Tumor |
Stage IIIA |
| TCGA-BR-7959-01A-11R-2343-13 |
TCGA-BR-7959 |
TP |
Primary solid Tumor |
Stage IIIA |
| TCGA-IN-8462-01A-11R-2343-13 |
TCGA-IN-8462 |
TP |
Primary solid Tumor |
Stage IIB |
| TCGA-BR-A4CR-01A-11R-A24K-31 |
TCGA-BR-A4CR |
TP |
Primary solid Tumor |
Stage IIIC |
| TCGA-CG-4443-01A-01R-1157-13 |
TCGA-CG-4443 |
TP |
Primary solid Tumor |
Stage IA |
| TCGA-KB-A93J-01A-11R-A39E-31 |
TCGA-KB-A93J |
TP |
Primary solid Tumor |
Stage II |
| TCGA-IN-A6RO-01A-12R-A33Y-31 |
TCGA-IN-A6RO |
TP |
Primary solid Tumor |
Stage IA |
| TCGA-HU-A4H3-01A-21R-A251-31 |
TCGA-HU-A4H3 |
TP |
Primary solid Tumor |
Stage IIIC |
| TCGA-RD-A8MV-01A-11R-A36D-31 |
TCGA-RD-A8MV |
TP |
Primary solid Tumor |
Stage IIIB |
使用命令举例：
Rscript subset_column.r -i ../01.TCGA_download/TCGA-STAD_gene_expression_TPM.tsv -m metadata.tsv -p TCGA-STAD_gene_expression_TPM
