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Edger_analysis.r differential gene analysis of edgeR

Usage: $Rscript $scriptdir/edger_analysis.r-husage: / work/my_stad_immu/scripts/edger_analysis.r [- h]-I filepath-m filepath-t treatname-- control CONTROL-- case CASE [- f fdr] [- c fc] [- s size] [- an alpha] [- X x.lab] [- Y y.lab] [- T title] [- H height] [- W width] [- o path] [- p prefix] edgeR analysis: https://www..com/article/1506optional arguments:-h -- help show this help message and exit-I filepath,-- input filepath input read count file [required]-m filepath,-- metadata filepath metadata file, required-t treatname,-- treatname treatname treat colname in group file, required-- control CONTROL set control group name required-- case CASE set case group name required-f fdr -- fdr fdr set fdr threshold [default 0.05]-- c fc,-- fc fc set fold change threshold [default 2]-s size,-- size size point size [optional, default: 0.7]-an alpha,-- alpha alpha point transparency [0-1] [optional, default: 1]-X x.lab,-- x.lab x.lab the label for x axis [optional Default: log2FC]-Y y.lab,-- y.lab y.lab the label for y axis [optional, default:-log10 (FDR)]-T title,-- title title the label for main title [optional, default: Volcano]-H height,-- height height the height of pic inches [default 5]-W width -- width width the width of pic inches [default 5]-o path,-- outdir path output file directory [default / work/my_stad_immu/05.enrich]-p prefix,-- prefix prefix out file name prefix [default Volcano] parameter description:

-I input the gene expression matrix file, which must be a count expression file:

IDTCGA-B7-A5TK-01A-12R-A36D-31TCGA-BR-7959-01A-11R-2343-13TCGA-IN-8462-01A-11R-2343-13TCGA-BR-A4CR-01A-11R-A24K-31TCGA-CG-4443-01A-01R-1157-13TCGA-KB-A93J-01A-11R-A39E-31TCGA-BR-4371-01A-01R-1157-13TSPAN65951403628343484253720274749TNMD3401018DPM14672433017254370652330944415SCYL31260205770214839241451982C1orf1125239921721400234733958FGR1249112728514856941208CFH12831114355387995457121891795FUCA25896785732085625152775303290GCLC2682550914479323642252652418

-m metadata file path, grouping information of the sample, the first column must correspond to the sample name of the expression file:

Barcodesubtype.hclustStromalScoreImmuneScoreESTIMATEScoreTumourPurityTCGA-B7-A5TK-01A-12R-A36D-31S11026.0572386.8353412.8920.448276TCGA-BR-7959-01A-11R-2343-13S21130.722729.4021860.1240.638667TCGA-IN-8462-01A-11R-2343-13S2112.2318683.9349796.16670.750581TCGA-BR-A4CR-01A-11R-A24K-31S2-1060.35-766.618-1826.970.943814TCGA-CG-4443-01A-01R-1157-13S2-261.577-258.629-520.2060.8635TCGA pay KBMI A93J- 01A-11R-A39E-31S1-202.2551605.121402.8650.688838TCGA-BR-4371-01A-01R-1157-13S2-828.231711.3379-116.8930.832147TCGA-IN-A6RO-01A-12R-A33Y-31S2-1406.5768.58307-1337.980.917683TCGA-HU-A4H3-01A-21R-A251-31S2-619.208538.7225-80.48540.829171TCGAmura A8MVMAFEN 01AUKEI 11RFEI A36DMAE 31S1113.41272309.6472423.060.572976TCGARAVQFI A91XM01A12RLYA414- 31S2-1845.85-590.017-2435.870.969545TCGA-D7-8575-01A-11R-2343-13S2-206.1121392.7991186.6870.711491TCGA-BR-4257-01A-01R-1131-13S1861.0291676.1482537.1770.559167TCGA-BR-8485-01A-11R-2402-13S1373.09611110.5161483.6120.680198TCGA-BR-4370-01A-01R-1157-13S11300.4951802.3273102.8220.488483

-t subtype.hclust-- case S1-- control S2: specify the name of the metadata grouping column, and the comparison group name in the grouping. If the grouping name has spaces, it should be enclosed in quotation marks: "Stage IA"

-- fdr 0.01-- fc 2 sets the screening conditions for differential genes: significance and multiple of differences

Use examples: Rscript $scriptdir/edger_analysis.r-I. / 01.TCGA_download/TCGA-STAD_gene_expression_Counts.tsv\-- fdr 0.01-- fc 2\-m.. / 03.TIME/metadata.group.tsv-t subtype.hclust-- case S1-- control S2-p S1_vs_S2 is the content of this article on "how to use edger_analysis.r in R language". I believe everyone has a certain understanding. I hope the content shared by the editor will be helpful to all of you. If you want to know more about the relevant knowledge, please follow the industry information channel.

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