buildPanel_oneCluster: Build panel for one cluster (beta)

In AllenInstitute/mfishtools: Building Gene Sets and Mapping mFISH Data

Build panel for one cluster (beta)

Description

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.

Usage

buildPanel_oneCluster(
  mapDat,
  clustersF,
  medianDat = NA,
  propIn = NA,
  clust = as.character(clustersF[1]),
  subSamp = NA,
  seed = 10,
  maxSize = 20,
  dexCutoff = 0.001,
  topGeneCount = 100
)

Arguments

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

Value

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.

AllenInstitute/mfishtools documentation built on July 5, 2023, 4:20 p.m.