selectFeatures {phemd} | R 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'))

[Package phemd version 1.0.1 Index]