buildMappingBasedMarkerPanel: Greedy algorithm for building marker gene panel
In AllenInstitute/mfishtools: Building Gene Sets and Mapping mFISH Data

buildMappingBasedMarkerPanel

R Documentation

Greedy algorithm for building marker gene panel

Description

This is the primary function that iteratively builds a marker gene panel, one gene at a time by iteratively adding the most informative gene to the existing gene panel.

Usage

buildMappingBasedMarkerPanel(
  mapDat,
  medianDat = NA,
  clustersF = NA,
  panelSize = 50,
  subSamp = 20,
  maxFcGene = 1000,
  qMin = 0.75,
  seed = 10,
  currentPanel = NULL,
  panelMin = 5,
  writeText = TRUE,
  corMapping = TRUE,
  optimize = "FractionCorrect",
  clusterDistance = NULL,
  clusterGenes = NULL,
  dend = NULL,
  percentSubset = 100
)

Arguments

`mapDat`	normalized data of the mapping (=reference) data set.
`medianDat`	representative value for each leaf. If not entered, it is calculated
`clustersF`	cluster calls for each cell.
`panelSize`	number of genes to include in the marker gene panel
`subSamp`	number of random nuclei to select from each cluster (to increase speed); set as NA to not subsample
`maxFcGene`	maximum number of genes to consider at each iteration (to increase speed)
`qMin`	minimum quantile for fold change comparison (between 0 and 1, higher = more specific marker genes are included)
`seed`	for reproducibility
`currentPanel`	starting panel. Default is NULL.
`panelMin`	if there are fewer genes than this, the top number of these genes by fc rank are set as the starting panel. Cannot be less than 2.
`writeText`	should gene names and marker scores be output (default TRUE)
`corMapping`	if TRUE (default) map by correlation; otherwise, map by Euclidean distance (not recommended)
`optimize`	if 'FractionCorrect' (default) will seek to maximize the fraction of cells correctly mapping to final clusters if 'CorrelationDistance' will seek to minimize the total distance between actual cluster calls and mapped clusters if 'DendrogramHeight' will seek to minimize the total dendrogram height between actual cluster calls and mapped clusters
`clusterDistance`	only used if optimize='CorrelationDistance'; a matrix (or vector) of cluster distances. Will be calculated if NULL and if clusterGenes provided. (NOTE: order must be the same as medianDat and/or have column and row names corresponding to clusters in clustersF)
`clusterGenes`	a vector of genes used to calculate the cluster distance. Only used if optimize='CorrelationDistance' and clusterDistance=NULL.
`dend`	only used if optimize='DendrogramHeight' dendrogram; will error out of not provided
`percentSubset`	for each iteration the function can subset the set of possible genes to speed up the calculation.