possibleClustersByPriors: Filter possible cluster calls using priors

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

Filter possible cluster calls using priors

Description

This function will return a vector of possible clusters for cells that meet a set of priors for each layer

Usage

possibleClustersByPriors(
  cluster,
  layer,
  subsetVector = rep(TRUE, length(cluster)),
  useClusters = sort(unique(cluster)),
  rareLimit = 0.005,
  layerNm = c("L1", "L2/3", "L4", "L5", "L6"),
  scaleByLayer = TRUE,
  scaleByFn = max,
  smartWeight = TRUE,
  spillFactor = 0.15,
  weightCutoff = 0.02
)

Arguments

cluster	vector of all clusters
layer	list of layers for each cluster entry (for data sets with only laminar dissections, each list entry will be of length 1)
subsetVector	a vector of TRUE/FALSE values indicated whether the entry is in the subset of interest (e.g., Cre lines); default is all
useClusters	a set of clusters to be considered a priori (e.g., GABA vs. glut); default is all
rareLimit	define any values less than this as 0. The idea is to exclude rare cells
layerNm	names of all layers. set to NULL to have this calculated
scaleByLayer	if TRUE, scales to the proportion of cells in each layer
scaleByFn	what function should be used for the layer scaling (default=max, ignored if scaleByLayer=FALSE)
smartWeight	if TRUE, multilayer dissections are weighted smartly by cluster, rather than evenly by cluster (FALSE)
spillFactor	fractional amount of cells in a layer below which it is assumed no cells are from that layer in multilayer dissection
weightCutoff	anything less than this is set to 0 for convenience

Value

a vector of possible clusters for cells that meet a set of priors for each layer

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