R/GEX_topN_DE_genes_per_cluster.R
GEX_topN_DE_genes_per_cluster.RdOrganizes the top N genes that define each Seurat cluster and converts them into a single dataframe. This can be useful for obtaining insight into cluster-specific phenotypes.
GEX_topN_DE_genes_per_cluster(GEX_cluster_genes.output, n.genes, by_FC, filter)The output from the GEX_cluster_genes function - this should be a list with each list element corresponding to the genes, p values, logFC, pct expression for the genes differentially regulated for each cluster.
The number of genes to be selected from each cluster. If n.genes is higher than the number of cells in a cluster then it is silently adjusted to be
Logical indicating if the top n genes are selected based on the logFC value instead of p value. Default is FALSE.
Character vector of initials of the genes to be filtered. Default is c("MT-", "RPL", "RPS"), which filters mitochondrial and ribosomal genes.
Returns a dataframe in which the top N genes defining each cluster based on differential expression are selected.
if (FALSE) {
GEX_topDE_genes_per_cluster(GEX_cluster_genes.output=list_of_genes_per_cluster
, n.genes=20, by_FC=FALSE, filter=c("MT-", "RPS", "RPL"))
}