aggreprobe-methods: Generate aggregated counts of probes for the same target

In Nanostring-Biostats/GeoDiff: Count model based differential expression and normalization on GeoMx RNA data

Generate aggregated counts of probes for the same target

Description

Generate Generate aggregated counts of probes for the same target, based on their score test results or correlation

Generate Generate aggregated counts of probes for the same target, based on their score test results or correlation

Usage

aggreprobe(object, ...)

## S4 method for signature 'NanoStringGeoMxSet'
aggreprobe(
  object,
  split,
  use = c("score", "cor", "both"),
  corcutoff = 0.85,
  ...
)

## S4 method for signature 'matrix'
aggreprobe(
  object,
  probenames,
  featurenames,
  negmod,
  use = c("score", "cor", "both"),
  corcutoff = 0.85,
  ...
)

Arguments

object	matrix of probes
...	additional argument list that might be used
split	indicator variable on whether it is for multiple slides (Yes, TRUE; No, FALSE)
use	the method to determine outliers including score, cor, and both
corcutoff	the cutoff value for correlation
probenames	vector of names of probe
featurenames	vector of names of features each probe corresponding to
negmod	Poisson Background model object for negative probes

Value

• remain, the list of remaining probes of targets

• probenum, numerical vector of probe numbers of targets

• featuremat, the matrix of features

• remain, the list of remaining probes of targets

• probenum, numerical vector of probe numbers of targets

• featuremat, the matrix of features

Examples

data("demoData")
demoData <- aggreprobe(demoData, use = "cor")

Nanostring-Biostats/GeoDiff documentation built on April 11, 2024, 5:31 a.m.