R语言怎么在metadata中添加基因表达数据

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merge_metadata_genexpdata.r  在metadata中添加基因表达数据

使用说明：

metadata添加基因表达结果。 基因表达文件行为不同基因，列为不同样本， 只要是列为不同样本的文件都可以用这个脚本合并到metadata中；

$Rscript $scriptdir/merge_metadata_genexpdata.r -h
usage: /share/nas1/huangls/test/TCGA_immu/scripts/merge_metadata_genexpdata.r
       [-h] -m metadata -g expset -b by [--log2] [-o outdir] [-p prefix]
merge metadata and gene expression：
optional arguments:
  -h, --help            show this help message and exit
  -m metadata, --metadata metadata
                        input metadata file path with suvival time [required]
  -g expset, --expset expset
                        input gene expression set file [required]
  -b by, --by by        input sample ID column name in metadata [required]
  --log2                whether do log2 transfrom for expression data
                        [optional, default: False]
  -o outdir, --outdir outdir
                        output file directory [default cwd]
  -p prefix, --prefix prefix
                        out file name prefix [default cox]

参数说明：

-m  指定metadata文件：

barcode	patient	sample	shortLetterCode	definition	sample_submitter_id	sample_type_id	sample_id	sample_type
TCGA-B7-A5TK-01A-12R-A36D-31	TCGA-B7-A5TK	TCGA-B7-A5TK-01A	TP	Primary solid Tumor	TCGA-B7-A5TK-01A	1	58937d2c-b4c3-4992-a95c-d0d1fa73f1a9	Primary Tumor
TCGA-BR-7959-01A-11R-2343-13	TCGA-BR-7959	TCGA-BR-7959-01A	TP	Primary solid Tumor	TCGA-BR-7959-01A	1	c8fc5fb2-ded2-48af-a87d-36c367a3330d	Primary Tumor
TCGA-IN-8462-01A-11R-2343-13	TCGA-IN-8462	TCGA-IN-8462-01A	TP	Primary solid Tumor	TCGA-IN-8462-01A	1	26509d1e-253b-463c-8654-589929889fbe	Primary Tumor
TCGA-BR-A4CR-01A-11R-A24K-31	TCGA-BR-A4CR	TCGA-BR-A4CR-01A	TP	Primary solid Tumor	TCGA-BR-A4CR-01A	1	76165733-85ca-47d0-a82a-f64fa9b1b834	Primary Tumor
TCGA-CG-4443-01A-01R-1157-13	TCGA-CG-4443	TCGA-CG-4443-01A	TP	Primary solid Tumor	TCGA-CG-4443-01A	1	f4fb736a-42c9-4367-a327-d0d1c4cba359	Primary Tumor
TCGA-KB-A93J-01A-11R-A39E-31	TCGA-KB-A93J	TCGA-KB-A93J-01A	TP	Primary solid Tumor	TCGA-KB-A93J-01A	1	888711a8-8ffd-49bb-aa85-7455c07f1ad5	Primary Tumor
TCGA-BR-4371-01A-01R-1157-13	TCGA-BR-4371	TCGA-BR-4371-01A	TP	Primary solid Tumor	TCGA-BR-4371-01A	1	95d6e839-a21b-4266-b7f8-e47fab262af3	Primary Tumor
TCGA-IN-A6RO-01A-12R-A33Y-31	TCGA-IN-A6RO	TCGA-IN-A6RO-01A	TP	Primary solid Tumor	TCGA-IN-A6RO-01A	1	c6e17043-a145-4cc3-b889-4f499b17dbf3	Primary Tumor
TCGA-HU-A4H3-01A-21R-A251-31	TCGA-HU-A4H3	TCGA-HU-A4H3-01A	TP	Primary solid Tumor	TCGA-HU-A4H3-01A	1	cd33e854-1bdf-42e0-83e7-256c723c5b55	Primary Tumor
TCGA-RD-A8MV-01A-11R-A36D-31	TCGA-RD-A8MV	TCGA-RD-A8MV-01A	TP	Primary solid Tumor	TCGA-RD-A8MV-01A	1	f7a464d1-9939-4ab8-a03b-f2962e618817	Primary Tumor
TCGA-VQ-A91X-01A-12R-A414-31	TCGA-VQ-A91X	TCGA-VQ-A91X-01A	TP	Primary solid Tumor	TCGA-VQ-A91X-01A	1	288b0130-6744-495e-bd99-da6f6b5f6953	Primary Tumor
TCGA-D7-8575-01A-11R-2343-13	TCGA-D7-8575	TCGA-D7-8575-01A	TP	Primary solid Tumor	TCGA-D7-8575-01A	1	71efd38a-03a9-488d-bde2-18b17559c775	Primary Tumor
TCGA-BR-4257-01A-01R-1131-13	TCGA-BR-4257	TCGA-BR-4257-01A	TP	Primary solid Tumor	TCGA-BR-4257-01A	1	97b44b05-97eb-486c-94db-42838831de0b	Primary Tumor
TCGA-BR-8485-01A-11R-2402-13	TCGA-BR-8485	TCGA-BR-8485-01A	TP	Primary solid Tumor	TCGA-BR-8485-01A	1	2f1460ea-827b-4c51-86a5-2d85771888bb	Primary Tumor
TCGA-BR-4370-01A-01R-1157-13	TCGA-BR-4370	TCGA-BR-4370-01A	TP	Primary solid Tumor	TCGA-BR-4370-01A	1	cfb7901b-e4e1-42fe-802d-dcd34f8c4912	Primary Tumor
TCGA-D7-A748-01A-12R-A32D-31	TCGA-D7-A748	TCGA-D7-A748-01A	TP	Primary solid Tumor	TCGA-D7-A748-01A	1	308bca2d-6e27-4da9-9a07-b0eb88437953	Primary Tumor
TCGA-VQ-A91Z-01A-11R-A414-31	TCGA-VQ-A91Z	TCGA-VQ-A91Z-01A	TP	Primary solid Tumor	TCGA-VQ-A91Z-01A	1	ec6ed61a-1d7e-4057-9ac2-dd1ed2accfb0	Primary Tumor
TCGA-RD-A7C1-01A-11R-A32D-31	TCGA-RD-A7C1	TCGA-RD-A7C1-01A	TP	Primary solid Tumor	TCGA-RD-A7C1-01A	1	b905ac72-aae1-4e6e-b560-46b9f4f9ef5f	Primary Tumor

-g  指定要合并的 文件：

cell_type	TCGA-B7-A5TK-01A-12R-A36D-31	TCGA-BR-7959-01A-11R-2343-13	TCGA-IN-8462-01A-11R-2343-13	TCGA-BR-A4CR-01A-11R-A24K-31	TCGA-CG-4443-01A-01R-1157-13	TCGA-KB-A93J-01A-11R-A39E-31	TCGA-BR-4371-01A-01R-1157-13	TCGA-IN-A6RO-01A-12R-A33Y-31	TCGA-HU-A4H3-01A-21R-A251-31	TCGA-RD-A8MV-01A-11R-A36D-31
B cells naive	0.041806	0.119034	0.275451	0.243789	0.118753	0.097526	0.087438	0.110736	0.091899	0.114157
B cells memory	0	0	0	0	0	0	0	0	0	0
Plasma cells	0.005778	0.009967	0.04908	0	0	0.009401	0.006596	0.012819	0.004326	0.001989
T cells CD8	0.399813	0.081383	0.052203	0.032568	0	0.017233	0.042146	0.074234	0.192331	0.10848
T cells CD4 naive	0	0	0	0	0	0	0	0	0	0
T cells CD4 memory resting	0	0.163605	0.158559	0.205805	0.161354	0.197031	0.445467	0.207407	0.095721	0.173691
T cells CD4 memory activated	0.222587	0.056429	0.022786	0.026488	0.008663	0.049117	0.016507	0.062309	0.132577	0.077914
T cells follicular helper	0.006564	0	0	0.007444	0	0.01711	0.009081	0.060454	0.040637	0.056979
T cells regulatory (Tregs)	0	0.034066	0.08263	0.040602	0.001932	0.038297	0	0.052859	0.052045	0.045091
T cells gamma delta	0	0	0	0	0	0.008108	0	0.00487	0	0
NK cells resting	0	0.034875	0	0.02808	0.031821	0	0.018045	0.006281	0.023437	0.029263
NK cells activated	0.00696	0	0.029651	0	0	0.047286	0	0.004472	0.007489	0
Monocytes	0.005411	0.013788	0.007133	0	0.02435	0.002008	0.013182	0	0	0.00139
Macrophages M0	0.014514	0.090352	0.025032	0.104725	0.16705	0.224299	0.078476	0.117533	0.068365	0.109002
Macrophages M1	0.135967	0.103223	0.100643	0.012271	0	0.080839	0.078876	0.122465	0.063667	0.103607
Macrophages M2	0.089259	0.159524	0.044703	0.137346	0.428193	0.156385	0.101052	0.10287	0.071646	0.077649
Dendritic cells resting	0.014316	0.019249	0.059299	0.006178	0	0.022708	0.043902	0	0	0.004566

使用举例：

将免疫浸润的结果合并到metadata中方便后续做比较分析：

Rscript $scriptdir/merge_metadata_genexpdata.r -m  ../08.Nomogram/nomogram_metadata.tsv -g ../03.TIME/immu/timer.res.tsv \
   -b barcode -p metadata_risk_score_timer

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