diagPoisBG | R Documentation |
Perform diagnosis on Poisson background model
Perform diagnosis on Poisson background model
diagPoisBG(object, ...) ## S4 method for signature 'NanoStringGeoMxSet' diagPoisBG( object, split = FALSE, padj = FALSE, padj_method = "BH", cutoff = 1e-06, generate_ppplot = TRUE ) ## S4 method for signature 'list' diagPoisBG( object, padj = FALSE, padj_method = "BH", cutoff = 1e-06, generate_ppplot = TRUE )
object |
a list of sizefact, featfact, countmat, or id (if it is for mutliple slides) |
... |
additional argument list that might be used |
split |
indicator variable on whether it is for multiple slides (Yes, TRUE; No, FALSE) |
padj |
whether to adjust p value for outlier detection, default =TRUE |
padj_method |
p value adjustment method, default ="BH" |
cutoff |
p value(or adjusted p value) cutoff to determine outliers |
generate_ppplot |
whether to generate ppplot, default =TRUE |
a valid S4 object
lowtail - A matrix of lower tail probabilty, in assay slot
uptail - A matrix of upper tail probability, in assay slot
disper (or disper_sp if non single-valued groupvar is provided) - dispersion parameter in experimenetData
low_outlier - A matrix to indicate lower outliers (0:False, 1:True) in assay slot
upper_outlier - A matrix to indicate upper outliers (0:False, 1:True) in assay slot
a list of following items
lowtail - A matrix of lower tail probabilty
uptail - A matrix of upper tail probability
disper - dispersion parameter
outlier - A list of coodinates of lower and upper outliers
data(demoData) demoData <- fitPoisBG(demoData, size_scale = "sum") demoData <- diagPoisBG(demoData) Biobase::notes(demoData)$disper demoData <- fitPoisBG(demoData, groupvar = "slide name") demoData <- diagPoisBG(demoData, split = TRUE) Biobase::notes(demoData)$disper_sp
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