Setting up the workflow and first steps24 days ago
Introduction | Setting up your workflow with dynamic vars | General approach | Tags | Mandatory IS vars | Annotation IS vars | Association file columns | VISPA2 stats specs | Customizing dynamic vars | FAQs | Do I have to do this every time the package loads? | Reporting progress | Introduction to ISAnalytics import functions family | Designed to work with VISPA2 pipeline | File system structure generated | Notation | Importing metadata | Function arguments | Importing VISPA2 stats files | Importing a single integration matrix | Automated integration matrices import | association_file argument | quantification_type argument | matrix_type argument | workers argument | multi_quant_matrix argument | report_path argument | mode argument | patterns argument | matching_opt argument | ... argument | Notes | Data cleaning and pre-processing | Removing collisions | What is a collision and why should you care? | The logic behind the function | Identifying the collisions | Re-assign vs remove | Usage | Re-align other matrices | Performing data and metadata aggregation | Aggregating metadata | Typical workflow | Aggregation of values by key | Changing parameters to obtain different results | Analysis use-case example: shared integration sites | Automated sharing counts | SCENARIO 1: single input data frame and single grouping key | Changing the number of comparisons | A case when it is useful to set minimal = FALSE | SCENARIO 2: single input data frame and multiple grouping keys | SCENARIO 3: multiple input data frame and single grouping key | SCENARIO 4: multiple input data frame and multiple grouping keys | Plotting sharing results | Reproducibility | Bibliography