Proposed Structure of Geomxtools - Nanostring-Biostats/GeomxTools GitHub Wiki

NanoStringGeomxset object related functions

  • class
    • option to be decided: add coercion from DSP-DA matrices to DCCset
  • read DCC
  • read PKC
  • accessors
  • subset
  • validity

Data Exploratory visualization functions

autoplot.NanoStringGeomxSet <- #wrapper function for plots for GeomxTools

  • spaceplot - call to spaceplot.R
  • SNRheatmap - call to heatmapSNR for every gene per AOI heatmap with proportion of detected genes per AOI

QC Plots

  • AOI QC Scatter plot - see AOI QC section

QC Related Functions

Inputs can be: NanoStringGeomxSet

Matrices - option to be decided: allow input for matrices from DSP-DA download (i.e. SegmentProperties, TargetProperties, TargetCountMatrix)

Wrapper Function to dispatch to corresponding QC method based on DCC type

  • switch datatype:
    • NGS
    • nCounter
    • protein
    • plexset

NGS QC

  • AOI QC
    • NegProbe counts vs Q9 counts and NegProbe counts vs Q9 to NegProbe Ratio scatter plots
      • input: quantile to use (defaults to Q9)
    • NegProbe Counts vs Number of Segments
    • Backgound QC for CTA spike-ins
    • remove AOI function
  • Gene QC
    • LOQ
  • Signal to background ratio QC

Protein QC

  • AOI QC - identify AOIs with poor data that should be removed (IgG geomean and HK geomean)

    • remove AOI function

  • Probe QC - identify poor performing probes by computing signal (AOI data) to background (IgG geomean) ratio per target

    • remove Probe

  • QC Plots: to be decided: do we put these in one function or together with the QC

    • AOI QC Plots
      • bar plots for AOI vs log2 (IgG or HK) geomean colored by scan ID and AOI Type
      • scatter plots HK geomean vs IgG geomean colored by scan ID and AOI type
    • Probe QC Plots
      • barplots of target vs Log2 Signal to background ratio with horizontal line on zero and vertical line

nCounter QC

(nctools)

plexset QC

(tbd)

Normalization related functions

Inputs can be: DCCsets

Matrices option to be decided: allow input for matrices from DSP-DA download (i.e. SegmentProperties, TargetProperties, TargetCountMatrix)

Wrapper Function to dispatch to corresponding normalization method based on DCC type

  • switch datatype:
    • NGS
    • nCounter
    • protein
    • plexset

NGS normalization

  • Q3 normalization
    • Q3 norm with background subtraction
  • Background norm
    • Background norm with background subtraction
  • area or nuclei scaling norm
  • Compare normalization
    • heatmap
    • PCA plots

protein normalization

  • Housekeeper norm
  • IgG norm
  • area norm
  • nuclei norm

nCounter normalization

(nctools)

plexset normalization

(tbd)

GeomxPlots

  • we can put all the plots here or assign them in each QC norm step