BGScoreTest | R Documentation |
Testing for features above the background using Poisson background model as reference
Testing for features above the background using Poisson background model as reference
BGScoreTest(object, ...) ## S4 method for signature 'NanoStringGeoMxSet' BGScoreTest( object, split = FALSE, adj = 1, removeoutlier = FALSE, useprior = FALSE ) ## S4 method for signature 'matrix' BGScoreTest( object, BGmod, adj = 1, probenum, removeoutlier = FALSE, useprior = FALSE )
object |
count matrix with features in rows and samples in columns |
... |
additional argument list that might be used |
split |
indicator variable on whether it is for multiple slides (Yes, TRUE; No, FALSE) |
adj |
adjustment factor for the number of feature in each gene, default =1 i.e. each target only consists of one probe |
removeoutlier |
whether to remove outlier |
useprior |
whether to use the prior that the expression level of background follows a Beta distribution, leading to a more conservative test |
BGmod |
a list of sizefact, sizefact, and countmat |
probenum |
a vector of numbers of probes in each gene |
a valid GeoMx S4 object including the following items
pvalues - Background score test pvalues, in featureData
scores - Background score test statistics, in featureData
if split is TRUE, a valid GeoMx S4 object including the following items
pvalues_XX - Background score test pvalues vector, column name (denoted as XX) the same as slide names, in featureData
scores_XX - Background score test statistics vector, column name (denoted as XX) the same as slide names, in featureData
a list of following items
pvalues - Background score test pvalues
scores - Background score test statistics
data(demoData) demoData <- fitPoisBG(demoData, size_scale = "sum") demoData <- aggreprobe(demoData, use = "cor") demoData <- BGScoreTest(demoData, adj = 1, useprior = FALSE) demoData <- fitPoisBG(demoData, size_scale = "sum", groupvar = "slide name") demoData <- BGScoreTest(demoData, adj = 1, useprior = TRUE, split = TRUE)
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