Hello! I am doing some single cell RNA seq analysis using Monocle3 software. Currently I have some Monocle objects in the form of cell data set objects that I want to look at.
I read in the RDS file into an R variable and from there, I looked at the rows and columns of my object.
monocle_object <- readRDS("monocle_cds.RDS")
class(monocle_object)
head(colData(monocle_object))
head(rowData(monocle_object))
I want to get all the values in the gene_short_name column in this monocle object (<character> type), so that I would get a list of all the possible gene short names in this monocle object. Does anyone have any suggestions on how I can do this? If there is an easy way to do this in R studio, I would like to know.
For this object, I also have a cell annotations text file, gene annotations text file and a umi counts matrix file (umi_counts.mtx). But I don't know if those would be useful for what I want to do here.
Any suggestions are greatly appreciated!
