View source: R/GEX_topN_DE_genes_per_cluster.R
GEX_topN_DE_genes_per_cluster | R Documentation |
Organizes 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)
GEX_cluster_genes.output |
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. |
n.genes |
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 |
by_FC |
Logical indicating if the top n genes are selected based on the logFC value instead of p value. Default is FALSE. |
filter |
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.
## Not run: 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")) ## End(Not run)
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