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This article mainly introduces the relevant knowledge of "how to use immune_infiltrates_rnaseq.r RNA-seq of R language". The editor shows you the operation process through an actual case. The operation method is simple, fast and practical. I hope this article "how to use immune_infiltrates_rnaseq.r RNA-seq of R language" can help you solve the problem.

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.

This is the end of quantiseqtimercibersortcibersort_absmcp_counterxcellepic 's introduction to "how to use immune_infiltrates_rnaseq.r RNA-seq in R language". Thank you for your reading. If you want to know more about the industry, you can follow the industry information channel. The editor will update different knowledge points for you every day.

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