matrixize_markers: Convert candidate genes list into matrix

In clustifyr: Classifier for Single-cell RNA-seq Using Cell Clusters

Description

Convert candidate genes list into matrix

Usage

matrixize_markers(
  marker_df,
  ranked = FALSE,
  n = NULL,
  step_weight = 1,
  background_weight = 0,
  unique = FALSE,
  metadata = NULL,
  cluster_col = "classified",
  remove_rp = FALSE
)

Arguments

marker_df	dataframe of candidate genes, must contain "gene" and "cluster" columns, or a matrix of gene names to convert to ranked
ranked	unranked gene list feeds into hyperp, the ranked gene list feeds into regular corr_coef
n	number of genes to use
step_weight	ranked genes are tranformed into pseudo expression by descending weight
background_weight	ranked genes are tranformed into pseudo expression with added weight
unique	whether to use only unique markers to 1 cluster
metadata	vector or dataframe of cluster names, should have column named cluster
cluster_col	column for cluster names to replace original cluster, if metadata is dataframe
remove_rp	do not include rps, rpl, rp1-9 in markers

Value

matrix of unranked gene marker names, or matrix of ranked expression

Examples

matrixize_markers(pbmc_markers)

clustifyr documentation built on Nov. 8, 2020, 5:32 p.m.