Get the compute result from a Microbiome Dataset in a particular format. Some formats may not be supported for all compute results.
Usage
getComputeResult(object, format = c("data.table"), ...)
# S4 method for ComputeResult
getComputeResult(object, format = c("data.table", "igraph"), ...)
# S4 method for CorrelationResult
getComputeResult(
object,
format = c("data.table", "igraph"),
correlationCoefThreshold = 0.5,
pValueThreshold = 0.05
)
# S4 method for DifferentialAbundanceResult
getComputeResult(object, format = c("data.table"))Arguments
- object
A Microbiome Dataset
- format
The format of the compute result. Currently only "data.table" and "igraph" are supported.
- ...
additional arguments passed to getComputeResult method of the subclasses of ComputeResult
- correlationCoefThreshold
threshold to filter edges by correlation coefficient. Edges with correlation coefficients below this threshold will be removed. Default is .5
- pValueThreshold
threshold to filter edges by p-value. Edges with p-values above this threshold will be removed. Default is .05
Examples
correlationOutput <- MicrobiomeDB::selfCorrelation(
getCollection(
microbiomeData::DiabImmune,
"16S (V4) Genus (Relative taxonomic abundance analysis)"),
method='spearman',
verbose=FALSE
)
#>
#> 2024-06-26 14:28:48.184477 Removed 1 records with no data.
#>
#> 2024-06-26 14:28:48.191186 Removed 1 records with no data.
correlationDT <- getComputeResult(correlationOutput, "data.table")
correlationIGraph <- getComputeResult(correlationOutput, "igraph")