summary_deviance {scGPS} | R Documentation

## get percent deviance explained for Lasso model, from `n` bootstraps

### Description

the training results from `training` were written to the object `LSOLDA_dat`, the `summary_devidance` summarises deviance explained for `n` bootstrap runs and also returns the best deviance matrix for plotting, as well as the best matrix with Lasso genes and coefficients

### Usage

    summary_deviance(object = NULL)

### Arguments

`object` | is a list containing the training results from `training`

### Value

a `list` containing three elements, with a vector of percent maximum deviance explained, a dataframe containg information for the full deviance, and a dataframe containing gene names and coefficients of the best model

### Author(s)

Quan Nguyen, 2017-11-25

### Examples

    c_selectID<-1
    day2 <- day_2_cardio_cell_sample
    mixedpop1 <-new_scGPS_object(ExpressionMatrix = day2$dat2_counts,
        GeneMetadata = day2$dat2geneInfo, CellMetadata = day2$dat2_clusters)
    day5 <- day_5_cardio_cell_sample
    mixedpop2 <-new_scGPS_object(ExpressionMatrix = day5$dat5_counts,
        GeneMetadata = day5$dat5geneInfo,
                        CellMetadata = day5$dat5_clusters)
    genes <-training_gene_sample
    genes <-genes$Merged_unique
    LSOLDA_dat <- bootstrap_prediction(nboots = 2,mixedpop1 = mixedpop1,
        mixedpop2 = mixedpop2, genes=genes, c_selectID, listData =list(),
        cluster_mixedpop1 = colData(mixedpop1)[,1],
        cluster_mixedpop2=colData(mixedpop2)[,1])
    summary_deviance(LSOLDA_dat)

[Package scGPS version 1.2.0 Index]