Mercurial > repos > caleb-easterly > peca
comparison peca.R @ 11:19bb06146c2e draft
planemo upload for repository https://github.com/caleb-easterly/galaxytools/peca
| author | caleb-easterly |
|---|---|
| date | Thu, 08 Mar 2018 18:27:44 -0500 |
| parents | e16cd77cf9f7 |
| children |
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| 10:f0de83932f9e | 11:19bb06146c2e |
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| 12 args <- commandArgs(trailingOnly = TRUE) | 12 args <- commandArgs(trailingOnly = TRUE) |
| 13 | 13 |
| 14 # read first argument, which is quant file (proteins in rows, samples in columns) | 14 # read first argument, which is quant file (proteins in rows, samples in columns) |
| 15 quant_file <- read.delim(args[1], | 15 quant_file <- read.delim(args[1], |
| 16 na.strings = c("0", "NA"), | 16 na.strings = c("0", "NA"), |
| 17 sep = '\t') | 17 sep = '\t', |
| 18 stringsAsFactors=FALSE) | |
| 18 | 19 |
| 19 # read 2nd and 3rd argument, which are path to files with group 1 and 2 column indices | 20 # read 2nd and 3rd argument, which are path to files with group 1 and 2 column indices |
| 20 group1_ind_file <- as.vector(as.matrix(read.csv(args[2], header = FALSE)[1, ])) | 21 group1_ind_file <- as.vector(as.matrix(read.csv(args[2], header = FALSE)[1, ])) |
| 21 group2_ind_file <- as.vector(as.matrix(read.csv(args[3], header = FALSE)[1, ])) | 22 group2_ind_file <- as.vector(as.matrix(read.csv(args[3], header = FALSE)[1, ])) |
| 22 | 23 |
| 23 # test type | 24 # test type |
| 24 ttype <- args[4] | 25 ttype <- args[4] |
| 25 | 26 |
| 26 # read 4th argument, which is output file name | 27 # paired or not |
| 27 out_file <- args[5] | 28 pair <- args[5] == "true" |
| 29 | |
| 30 # output file name | |
| 31 out_file <- args[6] | |
| 28 | 32 |
| 29 # get vectors of column names | 33 # get vectors of column names |
| 30 df_names <- colnames(quant_file) | 34 df_names <- colnames(quant_file) |
| 31 group1_names <- df_names[group1_ind_file] | 35 group1_names <- df_names[group1_ind_file] |
| 32 group2_names <- df_names[group2_ind_file] | 36 group2_names <- df_names[group2_ind_file] |
| 33 | 37 |
| 34 # run PECA_df | 38 # run PECA_df |
| 35 # id column is first column (hard-coded) | 39 # id column is first column (hard-coded) |
| 36 results <- PECA_df(quant_file, | 40 results <- PECA_df(df = quant_file, |
| 37 group1_names, | 41 samplenames1 = group1_names, |
| 38 group2_names, | 42 samplenames2 = group2_names, |
| 43 test = ttype, | |
| 44 paired = pair, | |
| 39 id = df_names[1]) | 45 id = df_names[1]) |
| 40 | 46 |
| 41 # put add protein names column | 47 # put add protein names column |
| 42 results$prot <- row.names(results) | 48 results$prot <- row.names(results) |
| 43 results <- results[, c("prot", "slr", "t", "score", "n", "p", "p.fdr")] | 49 results <- results[, c("prot", "slr", "t", "score", "n", "p", "p.fdr")] |