The function first removes genes without sufficient expression in any metacell minimal_max_log_fraction, or without sufficient fold
change over the median (minimal_relative_expression), and then ranks the fold change of genes within each metacell. The markers
are then the genes with the highest rank, up to n_genes genes.
Usage
get_rna_markers(
atac_mc,
n_genes = 100,
minimal_max_log_fraction = -13,
minimal_relative_log_fraction = 2,
fold_change_reg = 0.1,
genes = NULL,
rm_zeros = TRUE,
epsilon = 0.00001
)Arguments
- atac_mc
a McPeaks/McTracks object with RNA expression (using
add_mc_rna)- n_genes
maximal number of genes to return. Default: 100
- minimal_max_log_fraction
take only genes with at least one value (in log fraction units - normalized egc) above this threshold
- minimal_relative_log_fraction
take only genes with at least one value with relative log fraction (mc_fp) above this this value
- fold_change_reg
regularization factor for the fold change calculation (fold_change would be changed to
fold_change = fold_change + fold_change_reg)- genes
list of genes to match. Default (NULL): all genes
- rm_zeros
remove genes with no RNA expression in any metacell. Default: TRUE
- epsilon
regularization factor added to the log normalized expression