From e8db7225f8afb4254e5b635ccd8b9a89fa2bbb55 Mon Sep 17 00:00:00 2001
From: Danielle Callan <dcallan@upenn.edu>
Date: Mon, 29 Apr 2024 13:32:25 -0400
Subject: [PATCH] update tests and docs to reflect diff abund method name
 change

---
 man/internalDiffAbund-methods.Rd | 42 ++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)
 create mode 100644 man/internalDiffAbund-methods.Rd

diff --git a/man/internalDiffAbund-methods.Rd b/man/internalDiffAbund-methods.Rd
new file mode 100644
index 0000000..d2c7824
--- /dev/null
+++ b/man/internalDiffAbund-methods.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/method-differentialAbundance.R
+\name{internalDiffAbund}
+\alias{internalDiffAbund}
+\alias{internalDiffAbund,AbundanceData,Comparator-method}
+\title{Differential abundance}
+\usage{
+internalDiffAbund(
+  data,
+  comparator,
+  method = c("DESeq2", "Maaslin2"),
+  pValueFloor = P_VALUE_FLOOR,
+  verbose = c(TRUE, FALSE)
+)
+
+\S4method{internalDiffAbund}{AbundanceData,Comparator}(
+  data,
+  comparator,
+  method = c("DESeq2", "Maaslin2"),
+  pValueFloor = P_VALUE_FLOOR,
+  verbose = c(TRUE, FALSE)
+)
+}
+\arguments{
+\item{data}{AbsoluteAbundanceData object}
+
+\item{comparator}{Comparator object specifying the variable and values or bins to be used in dividing samples into groups.}
+
+\item{method}{string defining the the differential abundance method. Accepted values are 'DESeq2' and 'Maaslin2'.}
+
+\item{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.}
+
+\item{verbose}{boolean indicating if timed logging is desired}
+}
+\value{
+ComputeResult object
+}
+\description{
+This function returns the fold change and associated p value for a differential abundance analysis comparing samples in two groups.
+}