@sjcrh/proteinpaint-server 2.91.1-0 → 2.92.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/package.json +1 -1
- package/routes/termdb.DE.js +9 -5
- package/routes/termdb.singlecellSamples.js +1 -1
- package/src/app.js +301 -212
- package/utils/edge.R +10 -4
package/utils/edge.R
CHANGED
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@@ -114,14 +114,20 @@ keep <- filterByExpr(y, min.count = input$min_count, min.total.count = input$min
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114
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y <- y[keep, keep.lib.sizes = FALSE]
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115
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y <- calcNormFactors(y, method = "TMM")
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#print (y)
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117
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-
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117
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+
calculate_dispersion_time_start <- Sys.time()
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suppressWarnings({
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suppressMessages({
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dge <- estimateDisp(y = y)
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})
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})
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123
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+
calculate_dispersion_time_stop <- Sys.time()
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print("Dispersion Time")
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print (calculate_dispersion_time_stop - calculate_dispersion_time_start)
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126
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calculate_exact_test_time_start <- Sys.time()
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et <- exactTest(object = dge)
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124
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-
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128
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calculate_exact_test_time_stop <- Sys.time()
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print("Exact Time")
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print(calculate_exact_test_time_stop - calculate_exact_test_time_start)
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#print ("Time to calculate DE")
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#print (calculate_DE_time_stop - calculate_DE_time_start)
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#print (et)
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@@ -139,8 +145,8 @@ names(output)[2] <- "gene_symbol"
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names(output)[3] <- "fold_change"
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names(output)[4] <- "original_p_value"
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names(output)[5] <- "adjusted_p_value"
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-
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143
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-
toJSON(output)
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148
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#write_csv(output,"DE_output.txt")
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149
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cat(paste0("adjusted_p_values:",toJSON(output)))
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#output_json <- toJSON(output)
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#print ("output_json")
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#output_file <- paste0(input$output_path,"/r_output.txt")
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