/diff_analysis

Primary LanguageR

  • Description

    • R script for differential analysis to explore markers using wilcox-test and t-test

    • Example

    Rscript diff_analysis.R

    • Usage

      Rscript diff_analysis.R mat.table group.list W prefix outdir

      • first argument, mat.table: column is samples, row is taxon or ko

      • second argument, group.list format: first column is samples, second is groups

      • third argument, W or T or wilcox or t.test

      • forth argument, prefix of outfile

      • fifth argument, outdir

    #wilcox.test()
Rscript diff_analysis.R  input.table.xls group W prefix ./

#t.test()
Rscript diff_analysis.R  input.table.xls group T prefix ./

  • output file:

    ID: variable ids

    L1_mean: mean abundance of L1 group

    H2_mean: mean abundance of H2 group

    Diff: L1_mean - H2_mean

    FC(fold change): L1_mean/H2_mean

    W-stats or T-stats: Wilcox or T-test statistics

    p-value and q-value