seuratFindMarkers {singleCellTK} | R Documentation |
seuratFindMarkers
seuratFindMarkers( inSCE, cells1 = NULL, cells2 = NULL, group1 = NULL, group2 = NULL, allGroup = NULL, conserved = FALSE, test = "wilcox", onlyPos = FALSE, minPCT = 0.1, threshUse = 0.25, verbose = TRUE )
inSCE |
Input |
cells1 |
A |
cells2 |
A |
group1 |
Name of group1. |
group2 |
Name of group2. |
allGroup |
Name of all groups. |
conserved |
Logical value indicating if markers conserved between two
groups should be identified. Default is |
test |
Test to use for DE. Default |
onlyPos |
Logical value indicating if only positive markers should be returned. |
minPCT |
Numeric value indicating the minimum fraction of min.pct
cells in which genes are detected. Default is |
threshUse |
Numeric value indicating the logFC threshold value on
which on average, at least X-fold difference (log-scale) between the
two groups of cells exists. Default is |
verbose |
Logical value indicating if informative messages should
be displayed. Default is |
A SingleCellExperiment
object that contains marker genes
populated in a data.frame stored inside metadata slot.