| ... | ... |
@@ -9,8 +9,8 @@ runVAM( |
| 9 | 9 |
geneSetCollectionName, |
| 10 | 10 |
useAssay, |
| 11 | 11 |
resultNamePrefix = NULL, |
| 12 |
- center = TRUE, |
|
| 13 |
- gamma = FALSE |
|
| 12 |
+ center = FALSE, |
|
| 13 |
+ gamma = TRUE |
|
| 14 | 14 |
) |
| 15 | 15 |
} |
| 16 | 16 |
\arguments{
|
| ... | ... |
@@ -29,7 +29,7 @@ output matrices will be \code{resultNamePrefix_Distance} and
|
| 29 | 29 |
\code{"VAM_geneSetCollectionName_"} will be used. Default \code{NULL}.}
|
| 30 | 30 |
|
| 31 | 31 |
\item{center}{Boolean. If \code{TRUE}, values will be mean centered when
|
| 32 |
-computing the Mahalanobis statistic. Default \code{TRUE}.}
|
|
| 32 |
+computing the Mahalanobis statistic. Default \code{FALSE}.}
|
|
| 33 | 33 |
|
| 34 | 34 |
\item{gamma}{Boolean. If \code{TRUE}, a gamma distribution will be fit to
|
| 35 | 35 |
the non-zero squared Mahalanobis distances computed from a row-permuted |
| ... | ... |
@@ -37,7 +37,7 @@ version of the gene expression matrix. The estimated gamma distribution will |
| 37 | 37 |
be used to compute a one-sided p-value for each cell. If \code{FALSE}, the
|
| 38 | 38 |
p-value will be computed using the standard chi-square approximation for the |
| 39 | 39 |
squared Mahalanobis distance (or non-central if \code{center = FALSE}).
|
| 40 |
-Default \code{FALSE}.}
|
|
| 40 |
+Default \code{TRUE}.}
|
|
| 41 | 41 |
} |
| 42 | 42 |
\value{
|
| 43 | 43 |
A \linkS4class{SingleCellExperiment} object with VAM metrics stored
|
