Self Correlation

This function returns correlation coefficients for variables in one AbundanceData object against itself. It generally serves as a convenience wrapper around veupathUtils::correlation, with the exception that it additionally supports sparcc.

Usage

selfCorrelation(
  data,
  method = c("spearman", "pearson", "sparcc"),
  format = c("ComputeResult", "data.table"),
  verbose = c(TRUE, FALSE),
  ...
)

Arguments

data

An AbundanceData object

method

string defining the type of correlation to run. The currently supported values are 'spearman','pearson' and 'sparcc'

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

ComputeResult object

Examples

correlationDT <- selfCorrelation(
     getCollection(
  microbiomeData::DiabImmune, 
  "16S (V4) Genus (Relative taxonomic abundance analysis)"), 
     method = 'sparcc', 
     format = 'data.table'
)
#> 
#> 2024-06-26 14:29:07.33771 Removed 1 records with no data.
#> 
#> 2024-06-26 14:29:07.344699 Removed 1 records with no data.
#> 
#> 2024-06-26 14:29:07.351318 Removed 1 records with no data.
#> 
#> 2024-06-26 14:38:26.120324 Completed correlation with method=sparcc. Formatting results.
#> 
#> 2024-06-26 14:38:26.121569 Received df table with 3183 samples and 21 features with abundances.

correlationOutput <- selfCorrelation(
     getCollection(
  microbiomeData::DiabImmune, 
  "16S (V4) Genus (Relative taxonomic abundance analysis)"), 
     method = 'sparcc', 
     format = 'ComputeResult'
)
#> 
#> 2024-06-26 14:38:26.264025 Removed 1 records with no data.
#> 
#> 2024-06-26 14:38:26.270739 Removed 1 records with no data.
#> 
#> 2024-06-26 14:38:26.277149 Removed 1 records with no data.
#> 
#> 2024-06-26 14:47:43.940948 Completed correlation with method=sparcc. Formatting results.
#> 
#> 2024-06-26 14:47:43.942164 Received df table with 3183 samples and 21 features with abundances.
#> 
#> 2024-06-26 14:47:43.943521 Correlation computation completed with parameters recordIdColumn= 16S_rRNA_(V4)_assay_Id , method =  sparcc

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