scid_multiclass: Main function to get Gene expression matrix and signature...

In BatadaLab/scID: geneset-guided identification of cell types using single cell RNA-seq data

Description

Main function to get Gene expression matrix and signature genes and return matches and scores

Usage

scid_multiclass(
  target_gem = NULL,
  reference_gem = NULL,
  reference_clusters = NULL,
  markers = NULL,
  logFC = 0.5,
  normalize_reference = TRUE,
  estimate_weights_from_target = FALSE,
  weights = NULL,
  only_pos = FALSE
)

Arguments

target_gem	Data frame of gene expression (rows) per cell (columns) in target data
reference_gem	Data frame of gene expression (rows) per cell (columns) in reference data
reference_clusters	Named list of cluster IDs of reference cells
markers	Data frame of cluster specific genes that will be used instead of the reference data
logFC	LogFC threshold for extracting markers from reference clusters
normalize_reference	Logical to select if reference data need to be normalized (when raw counts have been provided)
only_pos	Logical to include negative markers in the cluster specific gene sets
use_reference_for_weights	Logical to use either reference or target data for sorting the signature genes

Value

list of cluster IDs for target cells

scID scores for target cells

markers used

estimated gene weights

BatadaLab/scID documentation built on Oct. 21, 2021, 3:06 p.m.