Correlation — correlation • MicrobiomeDB

This function returns correlation coefficients for variables in one dataset against variables in a second dataset

Usage

correlation(
  data1,
  data2,
  method,
  format = c("ComputeResult", "data.table"),
  verbose = c(TRUE, FALSE),
  ...
)

Arguments

data1: first dataset. A data.table
data2: second dataset. A data.table
method: string defining the type of correlation to run. The currently supported values are specific to the class of data1 and data2.
format: string defining the desired format of the result. The currently supported values are 'data.table' and 'ComputeResult'.
verbose: boolean indicating if timed logging is desired
...: additional parameters

Value

data.frame with correlation coefficients or a ComputeResult object

Examples

diabImmune_genus <- getCollection(
     microbiomeData::DiabImmune, 
     "16S (V4) Genus (Relative taxonomic abundance analysis)", 
     continuousMetadataOnly = TRUE
)

correlationDT <- correlation(
     diabImmune_genus, 
     method = 'spearman', 
     format = 'data.table'
)
#> 
#> 2024-06-26 14:27:50.6956 Completed correlation with method=spearman. Formatting results.
#> 
#> 2024-06-26 14:27:50.696787 Received df table with 3184 samples and 138 features with values.

correlationOutput <- correlation(
     diabImmune_genus, 
     method = 'spearman', 
     format = 'ComputeResult'
)
#> 
#> 2024-06-26 14:27:54.590912 Completed correlation with method=spearman. Formatting results.
#> 
#> 2024-06-26 14:27:54.591803 Received df table with 3184 samples and 138 features with values.
#> 
#> 2024-06-26 14:27:54.593337 Correlation computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method =  spearman

alsoCorrelationDT <- getComputeResult(
     correlationOutput, 
     "data.table"
)