GetTransferMatrix: Gets NN matrix for CITE->CODEX, stores in STvEA.data

In CamaraLab/STvEA: Spatially-resolved Transcriptomics via Epitope Anchoring

Gets NN matrix for CITE->CODEX, stores in STvEA.data

Description

Gets NN matrix for CITE->CODEX, stores in STvEA.data

Usage

GetTransferMatrix(
  stvea_object,
  k.cite = floor(nrow(stvea_object@corrected_codex) * 0.002),
  c.cite = 0.1,
  transfer.rna = TRUE,
  fastknn = FALSE
)

Arguments

stvea_object	STvEA.data class with mapping correction run
k.cite	number of nearest CODEX neighbors to find for each CITE-seq cell
c.cite	width of Gaussian kernel in CITE-seq dataset
fastknn	if set to TRUE, skips the computation of the NN matrix and uses the FastKNN library to transfer the CITE-seq labels into the CODEX data
transfer_rna	if set to TRUE (default), also transfers the mRNA data from CITE-seq to CODEX. Requires extra memory

CamaraLab/STvEA documentation built on April 2, 2024, 6:07 a.m.