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comparison goseq.r @ 11:602de62d995b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 0829a85b7fd9d09202450e50d30446cf9845791c
author iuc
date Wed, 11 Jan 2023 10:13:15 +0000
parents ef2ad746b589
children
comparison
equal deleted inserted replaced
10:43798b4caee0 11:602de62d995b
1 options(show.error.messages = F, error = function() { 1 options(show.error.messages = FALSE, error = function() {
2 cat(geterrmessage(), file = stderr()) 2 cat(geterrmessage(), file = stderr())
3 q("no", 1, F) 3 q("no", 1, FALSE)
4 }) 4 })
5 5
6 # we need that to not crash galaxy with an UTF8 error on German LC settings. 6 # we need that to not crash galaxy with an UTF8 error on German LC settings.
7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") 7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
8 8
144 p_adj_method = args$p_adj_method, 144 p_adj_method = args$p_adj_method,
145 out_fp = args$sampling_tab 145 out_fp = args$sampling_tab
146 ) 146 )
147 147
148 # Compare sampling with wallenius 148 # Compare sampling with wallenius
149 if (args$make_plots & !is.null(args$wallenius_tab)) { 149 if (args$make_plots && !is.null(args$wallenius_tab)) {
150 pdf(args$sample_vs_wallenius_plot) 150 pdf(args$sample_vs_wallenius_plot)
151 plot(log10(results[["Wallenius"]][, 2]), 151 plot(log10(results[["Wallenius"]][, 2]),
152 log10(results[["Sampling"]][match(results[["Sampling"]][, 1], results[["Wallenius"]][, 1]), 2]), 152 log10(results[["Sampling"]][match(results[["Sampling"]][, 1], results[["Wallenius"]][, 1]), 2]),
153 xlab = "log10(Wallenius p-values)", 153 xlab = "log10(Wallenius p-values)",
154 ylab = "log10(Sampling p-values)", 154 ylab = "log10(Sampling p-values)",