cellToClusterMapping_byCor: Return top mapped correlation-based cluster and confidence

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

Return top mapped correlation-based cluster and confidence

Description

Primary function for doing correlation-based mapping to cluster medians and also reporting the correlations and confidences. This is wrapper for getTopMatch and corTreeMapping.

Usage

cellToClusterMapping_byCor(
  medianDat,
  mapDat,
  refDat = NA,
  clusters = NA,
  genesToMap = rownames(mapDat),
  use = "p",
  method = "p",
  ...
)

Arguments

medianDat	representative value for each leaf and node. If not entered, it is calculated
mapDat	normalized data of the MAPPING data set. Default is to map the data onto itself.
refDat	normalized data of the REFERENCE data set. Ignored if medianDat is passed
clusters	cluster calls for each cell. Ignored if medianDat is passed
genesToMap	which genes to include in the correlation mapping
use	additional parameter for cor (use='p' as default)
method	additional parameter for cor (method='p' as default)
...	not used

Value

data frame with the top match and associated correlation

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