View source: R/markerGenesAndMapping.r
buildPanel_oneCluster | R Documentation |
This UNTESTED function finds the best small marker panel for marking a single cluster, using proportion difference as the metric for determining the starting panel.
buildPanel_oneCluster(
mapDat,
clustersF,
medianDat = NA,
propIn = NA,
clust = as.character(clustersF[1]),
subSamp = NA,
seed = 10,
maxSize = 20,
dexCutoff = 0.001,
topGeneCount = 100
)
mapDat |
normalized data of the mapping (=reference) data set. |
clustersF |
cluster calls for each cell. |
medianDat |
median value for each leaf |
propIn |
proportions of cells with expression > 1 in each leaf |
clust |
which cluster to target? |
subSamp |
number of random nuclei to select from each cluster, EXCEPT the target cluster; set as NA to not subsample |
seed |
for reproducibility |
maxSize |
maximum size of marker gene panel |
dexCutoff |
criteria for stopping: when improvement in fraction of cells properly mapped dips below this value |
topGeneCount |
number of top genes by proportion to consider |
a matrix of the top marker genes for each cluster. Output matrix includes five columns: clust = cluster; panel = ordered genes in the panel for that cluster; onCorrect = fraction of correctly assigned cells in cluster; offCorrect = fraction of cells correctly assigned outside of cluster; dexTotal = additional dex explained by last gene added.
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