selectFeatures {phemd} | R Documentation |
Takes as input a Phemd object with aggregated data and returns updated object after performing feature selection on aggregated data
selectFeatures(obj, selected_genes)
obj |
'Phemd' object containing aggregated data |
selected_genes |
Vector containing names of genes to use for downstream analyses |
aggregateSamples
needs to be called before running this function
Same as input 'Phemd' object after performing feature-selection based dimensionality reduction on aggregated expression data
my_phemdObj <- createDataObj(all_expn_data, all_genes, as.character(snames_data)) my_phemdObj_lg <- removeTinySamples(my_phemdObj, 10) my_phemdObj_lg <- aggregateSamples(my_phemdObj_lg, max_cells=1000) my_phemdObj_lg <- selectFeatures(my_phemdObj_lg, selected_genes=c('TP53', 'EGFR', 'KRAS', 'FOXP3', 'LAG3'))