Filtering NanoStringGeoMxSet dataset

Source: R/filtering.R

Function for filtering NanoStringGeoMxSet dataset

filtering(
  object,
  loq.cutoff = 2,
  loq.min = 2,
  segment.gene.rate.cutoff = 0.05,
  study.gene.rate.cutoff = 0.05,
  sankey.exclude.slide = FALSE,
  goi
)

Arguments

object

A NanoStringGeoMxSet dataset

loq.cutoff

The number of standard deviations above the negative probe geometric mean to use as a cutoff for the limit of quantification

loq.min

The minimum value for the limit of quantification

segment.gene.rate.cutoff

A decimal for the minimum cutoff for the genes detected in a given segment over the total number of genes in the probe set

study.gene.rate.cutoff

= A decimal for the minimum cutoff for the average amount a given gene is detected in all segments

sankey.exclude.slide

A toggle for including the slide name in the Sankey Plot

goi

A list of genes of interest to evaluate for their study-wide detection rate

Value

A list containing the ....

Details

Normalize Nano String Digital Spatial Profile

This function will run various filtering parameters for NanoStringGeoMxSet datasets