derive_GeoMx_background {SpatialDecon} | R Documentation |
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.
derive_GeoMx_background(norm, probepool, negnames)
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. |
A matrix of expected background values, in the same scale and dimensions as the "norm" argument.
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" )