How to use immune_infiltrates_rnaseq.r RNA-seq in R language
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Analysis of immune invasion of immune_infiltrates_rnaseq.r RNA-seq transcriptome data
Usage: $Rscript immune_infiltrates_rnaseq.r-husage: immune_infiltrates_rnaseq.r [- h]-I expset [- g gene.info] [- t type] [--tpm] [- o outdir] RNA seq immunoinvasiveness assay. In general values should be TPM-normalized, not log-transformed.optional arguments:-h,-- help show this help message and exit-I expset,-- expset expset input gene expression set matrix from RNA-seq data tsv format [required]-g gene.info,-- gene.info gene.info input gene info data [required]-t type -- type type TIMER uses indication-specific reference profiles. [optional]-- tpm whether convert fpkm to tpm [optional, default: False]-o outdir,-- outdir outdir output file directory [default cwd] parameter description:
-I input the gene expression file. It is recommended to use the standardized data of TPM. If it is FPKM, you can set-tpm for conversion. The first column of ID is gene NAME.
IDTCGA-D7-A74A-01A-11R-A32D-31TCGA-BR-7704-01A-11R-2055-13TCGA-VQ-A91N-01A-11R-A414-31TCGA-CD-A4MH-01A-11R-A251-31NUP5018.6550531.5923228.2338228.76485CXCR464.85805125.12356.3524469.98976NT5E111.481869.858779.3738225.05824EFNA38.24785742.0330843.4643226.66024STC14.78111121.3632740.8107719.51568ZBTB7A95.51678103.4768158.3024126.2677CLDN91.1874562.4761380.3660817.347344
-t specifies the cancer type, which is required for TIMER calculation. You can specify the type. If you do not specify not to output the analysis results of TIMER:
# "kich", "blca", "brca", "cesc", "gbm", "hnsc", "kirp", "lgg", "lihc"luad"
# "lusc", "prad", "sarc", "pcpg", "paad", "tgct", "ucec", "ov", "skcm"dlbc"
# "kirc", "acc", "meso", "thca", "uvm", "ucs", "thym", "esca", "stad"read"
# "coad"chol"
Method description:
Use R package: immunedeconv
The immune invasion analysis results of the following methods can be output. Mcp_counter needs to be connected to the network to run, and sometimes the wrong results can not be reported.
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