Transform Count Data in a Microbiome Dataset
Usage
transform_counts(
object,
method = c("relative", "log", "presence_absence", "clr"),
pseudocount = 1,
...
)
# S3 method for class 'microbiome_dataset'
transform_counts(
object,
method = c("relative", "log", "presence_absence", "clr"),
pseudocount = 1,
...
)
Arguments
- object
A microbiome_dataset object.
- method
Transformation method.
- pseudocount
A pseudocount added before transformations that require
strictly positive values.
- ...
Other parameters.
Value
A transformed microbiome_dataset object.
Examples
data("global_patterns", package = "microbiomedataset")
x <- transform_counts(global_patterns, method = "relative")
attr(x@expression_data, "counts_or_relative")
#> [1] "relative"
y <- transform_counts(global_patterns, method = "log", pseudocount = 1)
attr(y@expression_data, "transform_method")
#> [1] "log"
