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This article mainly introduces "how to use ppi_network.r in R language". In daily operation, I believe many people have doubts about how to use ppi_network.r in R language. The editor consulted all kinds of materials and sorted out simple and easy-to-use operation methods. I hope it will be helpful to answer the doubts about "how to use ppi_network.r in R language". Next, please follow the editor to study!

Analysis of ppi_network.r protein interaction network

Instructions: $Rscript $scriptdir/ppi_network.r-husage: / work/my_stad_immu/scripts/ppi_network.r [- h]-g gene.list [- s ann.db] [- t score_threshold] [- v version] [- p prefix] [- o outdir] [- H height] [- W width] GO enrich analysisoptional arguments:-h -- help show this help message and exit-g gene.list,-- gene.list gene.list diff expressed gene list file, required-s ann.db,-- species ann.db NCBI taxonomy identifiers of the organism (e.g. 9606 for Human, 10090 for mouse). Default 9606-t score_threshold,-- score_threshold score_threshold a threshold for the combined scores of the interactions, such that any interaction below that threshold is not loaded in the network (by default the score threshold is set to 700)-v version,-- version version define the STRING version to be used [optional Default: 11]-p prefix,-- prefix prefix the output file prefix [optional, default: PPI]-o outdir,-- outdir outdir output file directory [default cwd]-H height,-- height height the height of pic inches [default 10]-W width -- width width the width of pic inches [default 10] parameter description:

-g specify that the gene list file is SYMBOL ID: read the first column of the file ID list: STRING database to get the network

Use example: Rscript $scriptdir/ppi_network.r-g. / 04.deg/S1_vs_S2.DEG.final.tsv-p S1_vs_S2. At this point, the study of "how to use ppi_network.r in R language" is over. I hope I can solve your doubts. The collocation of theory and practice can better help you learn, go and try it! If you want to continue to learn more related knowledge, please continue to follow the website, the editor will continue to work hard to bring you more practical articles!

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