comparison goseq.r @ 19:9442d1bf6d93 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty

18:5fb82111ec62

    make_option(c("-sw","--sample_vs_wallenius_plot"), type="character", default=FALSE, help="Path to plot comparing sampling with wallenius p-values."),
    make_option(c("-padj", "--p_adj_column"), type="integer",help="Column that contains p. adjust values"),
    make_option(c("-c", "--cutoff"), type="double",dest="p_adj_cutoff",
                help="Genes with p.adjust below cutoff are considered not differentially expressed and serve as control genes"),
    make_option(c("-r", "--repcnt"), type="integer", default=100, help="Number of repeats for sampling"),
    make_option(c("-lf", "--length_file"), default=FALSE, help = "Path to "),
    make_option(c("-g", "--genome"), type="character", help = "Genome [used for looking up correct gene length]"),
    make_option(c("-i", "--gene_id"), type="character", help="Gene ID of gene column in DGE file")
  )
parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
args = parse_args(parser)

dge_table = read.delim(dge_file, header = TRUE, sep="\t", check.names = FALSE)
genes = as.integer(dge_table[,p_adj_column]<p_adj_cutoff)
names(genes) = dge_table[,1] # Assuming first row contains gene names

# Get gene lengths
if (length_file !=FALSE) {
  length_table = read.delim(length_file, header=TRUE, sep="\t", check.names=FALSE, row.names=TRUE)
  gene_lengths = length_table[names(genes),]$length
  } else {
  gene_lengths = getlength(names(genes), genome, gene_id)
  }

19:9442d1bf6d93

    make_option(c("-sw","--sample_vs_wallenius_plot"), type="character", default=FALSE, help="Path to plot comparing sampling with wallenius p-values."),
    make_option(c("-padj", "--p_adj_column"), type="integer",help="Column that contains p. adjust values"),
    make_option(c("-c", "--cutoff"), type="double",dest="p_adj_cutoff",
                help="Genes with p.adjust below cutoff are considered not differentially expressed and serve as control genes"),
    make_option(c("-r", "--repcnt"), type="integer", default=100, help="Number of repeats for sampling"),
    make_option(c("-lf", "--length_file"), type="character", default="FALSE", help = "Path to tabular file mapping gene id to length"),
    make_option(c("-g", "--genome"), type="character", help = "Genome [used for looking up correct gene length]"),
    make_option(c("-i", "--gene_id"), type="character", help="Gene ID of gene column in DGE file")
  )
parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
args = parse_args(parser)

dge_table = read.delim(dge_file, header = TRUE, sep="\t", check.names = FALSE)
genes = as.integer(dge_table[,p_adj_column]<p_adj_cutoff)
names(genes) = dge_table[,1] # Assuming first row contains gene names

# Get gene lengths
if (length_file != "FALSE" ) {
  length_table = read.delim(length_file, header=TRUE, sep="\t", check.names=FALSE)
  row.names(length_table) = length_table[,1]
  gene_lengths = length_table[names(genes),]$length
  } else {
  gene_lengths = getlength(names(genes), genome, gene_id)
  }