selectFeatures: Perform feature selection on aggregated data

In KrishnaswamyLab/phemd: Phenotypic EMD for comparison of single-cell samples

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 Oct. 2, 2024, 5:10 a.m.