selectFeatures: Perform feature selection on aggregated data

View source: R/functions-core.R

selectFeaturesR Documentation

Perform feature selection on aggregated data

Description

Takes as input a Phemd object with aggregated data and returns updated object after performing feature selection on aggregated data

Usage

selectFeatures(obj, selected_genes)

Arguments

obj

'Phemd' object containing aggregated data

selected_genes

Vector containing names of genes to use for downstream analyses

Details

aggregateSamples needs to be called before running this function

Value

Same as input 'Phemd' object after performing feature-selection based dimensionality reduction on aggregated expression data

Examples


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'))


KrishnaswamyLab/phemd documentation built on April 24, 2023, 3:50 p.m.