Preprocess #469
Preprocess #469
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| return(list( | ||
| data = tmm_proccessing(data, omic_type) | ||
| )) | ||
| } |
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Error: Error in DGEList(counts = assay(data)): could not find function "DGEList"
I assume we need to add a package to the renv?
| print(paste0("Remove anything of rowCount <=",filter_threshold_samplewise," in at least ",filter_samplesize," samples")) | ||
| return(data[which(rowSums(assay(data) > filter_threshold_samplewise) >= filter_samplesize),]) | ||
| } | ||
| } |
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I honestly thought we would replace the "prefiltering" option and instead always have the option of prefiltering. I think this would make sense as filtering is not entirely but partially independent of the user.
| data <- prefiltering(data, omic_type) | ||
| # Create DGEList object | ||
| dge <- DGEList(counts = assay(data)) | ||
| # TODO visulaize norn factor distribution |
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Is this a necessary todo still? We could think about putting this on top of the function since in the future, comments in out functions will be added to util in code generation.
| )%>% helper(type = "markdown", content = "PreProcessing_Procedures"), | ||
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| # Second dropdown: Options based on Processing Type | ||
| uiOutput(outputId = "dynamic_options_ui"), |
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We can do it like this, i have however noticed faster performance with UI elements directly defined in the UI through conditional panels. This is something we should definitely do at some point more rigorously but for review optional
| "<br>",ifelse(any(as.data.frame(assay(data)) < 0),"Be aware that processed data has negative values, hence no log fold changes can be calculated","")) | ||
| "<br>",ifelse(input$processing_type == "Log-Based","In case of 0's present logX(data+1) is done",""), | ||
| "<br>","See help for details", | ||
| "<br>",ifelse(any(as.data.frame(assay(data)) < 0),"Be aware that processed data has negative values!",""), ## IS THAT TRUE?? |
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from what i can see in the violin plot: yes, i think the comment can be removed
| filter_threshold = filter_threshold, | ||
| filter_threshold_samplewise = filter_threshold_samplewise, | ||
| filter_samplesize = filter_samplesize, | ||
| limma_intercept = limma_intercept, | ||
| limma_formula = limma_formula | ||
| ) |
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these need to be added to par_tmp for pre_processing to work
# Conflicts: # program/shinyApp/R/pre_processing/util.R # program/shinyApp/server.R
addressing #429
Opened #468 for main documentaion update incl. desicion tree which is still missing