get.ct.ps: Get celltype p-values

In NathanSkene/PatchseqMap: PatchseqMap

Description

Evaluates for cell type 'i' which of the reference cell types it is most likely to be. The probability values are returned as a vector.

Usage

get.ct.ps(cellTypesToConsider, specificity, hitGenes, patchCellI, patchSeqExp,
  bg)

Arguments

cellTypesToConsider	List of strings for cell type names from the reference dataset
specificity	A specificity matrix, generally for level2 celltypes, obtained using EWCE (only the specificity matrix (not the ctd) should be passed)
hitGenes	Genes which fulfull the following criteria: (1) Expressed in the reduced patchseq dataset, i.e. they have standard deviation over a given threshold; (2) They have at least one read in patchseq cell 'i'; (3) They are found in both patchseq and specificity datasets
patchCellI	Index of which patchseq cell is being considered
patchSeqExp	Gene by Cell matrix of the patchseq data
bg	Vector of gene symbols. All of these must be in the specificity matrix.

Value

A vector of p-values corresponding to cellTypesToConsider, where lowest value indicates that celltype is the most likely type for cell i

Examples

plot_crayons()

NathanSkene/PatchseqMap documentation built on May 17, 2019, 1:35 p.m.