Outputs

MCNV2 generates two types of outputs: visualizations (plots) for exploring Mendelian Precision patterns, and downloadable tables for downstream analyses.

Visualizations

MCNV2 provides interactive plots to assess CNV quality and identify optimal filtering strategies.

MP by size range (bar plots)

Description:

Bar plots showing Mendelian Precision for each CNV size range.

Axes:

  • X-axis: Size ranges (1-30kb, 30-50kb, 50-100kb, 100-200kb, 200-500kb, 500kb-1Mb, >1Mb)

  • Y-axis: Mendelian Precision (%)

Data displayed:

  • Separate plots for deletions (DEL) and duplications (DUP)

  • Bar height represents MP

  • Number on top of each bar shows CNV count (n)

Use case:

Identify size ranges with low MP that may benefit from filtering or exclusion.

MP versus quality score (line plots)

Description:

Line plots showing Mendelian Precision as a function of quality score threshold stratified by size range.

Axes:

  • X-axis: Quality score threshold (e.g., Score ≥ 0, 10, 20, …, 200)

  • Y-axis: Mendelian Precision (%)

Data displayed:

  • One line per size range (color-coded as above)

  • Each point represents MP when applying quality score threshold ≥ X

  • Separate plots for deletions (DEL) and duplications (DUP)

Legend:

Right side of plot shows:

  • n — Total CNV count for each size range

  • CNV Length — Size range label with marker symbol

  • Marker symbols: circles, triangles, plus signs, crosses, diamonds, etc.

Interpretation:

  • Plateau pattern: MP increases rapidly, then plateaus

  • Optimal threshold: Lowest value where plateau is reached

  • Divergent curves: Different size ranges require different thresholds

Interactive features:

  • Hover: Tooltip shows threshold value, MP, size range, and CNV count

  • Click legend: Show/hide specific size range curves

  • Zoom: Select area to zoom in

  • Download: Export as PNG, PDF, or SVG

Use case:

Identify optimal quality score thresholds for each size range.

Plot interactivity

Hover tooltips:

When hovering over data points, a tooltip displays:

  • threshold: Quality score value

  • MP: Mendelian Precision at this threshold

  • Size_Range: CNV size category

  • n: Number of CNVs remaining after applying filter

Multiple simultaneous tooltips:

Hovering near multiple curves shows tooltips for all size ranges at that threshold, enabling direct comparison.

Legend interaction:

Click on size range labels in the legend to show/hide curves. Useful for focusing on specific size categories.

Zoom and pan:

  • Box select: Click and drag to zoom into a region

  • Reset: Double-click to reset zoom

  • Pan: Shift + drag to move view

Download options:

Click camera icon to download plot as:

  • PNG (raster image)

Comparative plots (Fine-tuning)

Before vs After:

Fine-tuning displays up to 4 plots simultaneously:

  1. Before additional filters — Baseline MP (from MP Exploration)

  2. After additional filters — MP after applying Fine-tuning filters

  3. After + subset 1 — MP after filters + subset (e.g., Genic only)

  4. After + subset 2 — MP after filters + subset (e.g., Intergenic only)

Purpose:

  • Assess impact of additional filters

  • Compare genic vs intergenic MP

  • Evaluate subset-specific patterns

Zoom modal:

Click + button on any plot to view it enlarged in a modal window with:

  • Full-screen visualization

  • Enhanced interactivity

  • Download table button (green)

  • Close button

Downloadable tables

MCNV2 provides downloadable tables at multiple stages of analysis.

MP Exploration table

Location:

MP Exploration interface → “Filtered table” tab → Download CSV button

Content:

All CNVs passing the applied filters (size, transcript overlap, problematic regions, LOEUF).

Columns:

  • Original CNV columns: CHR, START, STOP, TYPE, SAMPLE_ID, quality scores

  • Annotation columns: GeneName, GeneID, Transcript, LOEUF, problematic_region_overlap

  • Inheritance columns: Transmitted_CNV (True/False), Transmitted_gene (True/False/intergenic)

  • Additional columns: TrioKey, family_statue, cnv_id, Size_Range, transmission

Row structure:

  • One row per CNV-gene pair (CNVs overlapping multiple genes have multiple rows)

  • Intergenic CNVs have empty gene columns

Use case:

  • Downstream statistical analyses

  • Manual inspection of specific CNVs

  • Integration with other genomic datasets

Export workflow

MP Exploration

Step 1: Apply filters using sliders and dropdowns

Step 2: Click “Apply filters” button

Step 3: Navigate to “Filtered table” tab

Step 4: Click “Download CSV” button

Step 5: Save file to desired location

Filename format: cnvs_filtered_<timestamp>.csv

Fine-tuning

Step 1: Apply advanced filters using dropdowns and value fields

Step 2: Click “Apply filters” button

Step 3: Click + button on desired plot (Before, After, or subset)

Step 4: In enlarged modal, click green “Download table” button

Step 5: Save file to desired location

Filename format: cnvs_finetuned_<condition>_<timestamp>.csv

See also