comparison peca.R @ 5:5a39fa8a235a draft

planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca

4:07bd2582526b

    # read 2nd and 3rd argument, which are path to files with group 1 and 2 column indices 
    group1_ind_file <- as.vector(as.matrix(read.csv(args[2], header = FALSE)[1, ]))
    group2_ind_file <- as.vector(as.matrix(read.csv(args[3], header = FALSE)[1, ]))

    # read 4th argument, which is output file name
    out_file <- args[4]

    # get vectors of column names
    df_names <- colnames(quant_file)
    group1_names <- df_names[group1_ind_file]
    group2_names <- df_names[group2_ind_file]
 
    # run PECA_df
    # id column is first column (hard-coded)
    results <- PECA_df(quant_file, group1_names, group2_names, id = df_names[1])

    # put add protein names column
    results$prot <- row.names(results)
    results <- results[, c("prot", "slr", "t", "score", "n", "p", "p.fdr")]
 

5:5a39fa8a235a

    # read 2nd and 3rd argument, which are path to files with group 1 and 2 column indices 
    group1_ind_file <- as.vector(as.matrix(read.csv(args[2], header = FALSE)[1, ]))
    group2_ind_file <- as.vector(as.matrix(read.csv(args[3], header = FALSE)[1, ]))

    # test type
    ttype <- args[4]

    # read 4th argument, which is output file name
    out_file <- args[5]

    # get vectors of column names
    df_names <- colnames(quant_file)
    group1_names <- df_names[group1_ind_file]
    group2_names <- df_names[group2_ind_file]
 
    # run PECA_df
    # id column is first column (hard-coded)
    results <- PECA_df(quant_file,
                group1_names,
                group2_names,
                type=ttype,
                id = df_names[1])

    # put add protein names column
    results$prot <- row.names(results)
    results <- results[, c("prot", "slr", "t", "score", "n", "p", "p.fdr")]