derive_GeoMx_background: Derive background at the scale of the normalized data for...

Description Usage Arguments Value Examples

View source: R/derive_GeoMx_background.R

Description

Estimates per-datapoint background levels from a GeoMx experiment. In studies with two or more probe pools, different probes will have different background levels. This function provides a convenient way to account for this phenomenon.

Usage

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derive_GeoMx_background(norm, probepool, negnames)

Arguments

norm

Matrix of normalized data, genes in rows and segments in columns. Must include negprobes, and must have rownames.

probepool

Vector of probe pool names for each gene, aligned to the rows of "norm".

negnames

Names of all negProbes in the dataset. Must be at least one neg.name within each probe pool.

Value

A matrix of expected background values, in the same scale and dimensions as the "norm" argument.

Examples

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data(mini_geomx_dataset)
# estimate background:
mini_geomx_dataset$bg <- derive_GeoMx_background(
  norm = mini_geomx_dataset$normalized,
  probepool = rep(1, nrow(mini_geomx_dataset$normalized)),
  negnames = "NegProbe"
)

SpatialDecon documentation built on Nov. 8, 2020, 6 p.m.