Finds markers (differentially expressed genes) for cell clusters using MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data (Finak et al, Genome Biology, 2015)
diffExpBetweenCellStates(counts, celda.mod, c1, c2 = NULL, only.pos = FALSE,
log2fc.threshold = NULL, fdr.threshold = 1)A numeric count matrix.
An object of class celda_C or celda_CG.
Numeric. Cell cluster(s) to define markers for.
Numeric. Second cell cluster(s) for comparison. If NULL (default) - use all other cells for comparison.
Logical. Only return markers with positive log2fc (FALSE by default).
Numeric. Only return markers whose the absolute values of log2fc are greater than this threshold (NULL by default).
Numeric. Only return markers whose false discovery rates (FDRs) are less than this threshold (1 by default).
Data frame containing a ranked list (based on the absolute value of log2fc) of putative markers, and associated statistics (p-value, log2fc and FDR).