This function returns the fold change and associated p value for a differential abundance analysis comparing samples in two groups.
Usage
internalDiffAbund(
data,
comparator,
method = c("DESeq2", "Maaslin2"),
pValueFloor = P_VALUE_FLOOR,
verbose = c(TRUE, FALSE)
)
# S4 method for class 'AbundanceData,Comparator'
internalDiffAbund(
data,
comparator,
method = c("DESeq2", "Maaslin2"),
pValueFloor = P_VALUE_FLOOR,
verbose = c(TRUE, FALSE)
)Arguments
- data
AbsoluteAbundanceData object
- comparator
Comparator object specifying the variable and values or bins to be used in dividing samples into groups.
- method
string defining the the differential abundance method. Accepted values are 'DESeq2' and 'Maaslin2'.
- pValueFloor
numeric value that indicates the smallest p value that should be returned. The corresponding adjusted p value floor will also be updated based on this value, and will be set to the maximum adjusted p value of all floored p values. The default value uses the P_VALUE_FLOOR=1e-200 constant defined in this package.
- verbose
boolean indicating if timed logging is desired