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Remove user-specified proteins (features) from a data frame

Source: R/modelProteins.R
rem_feature.Rd

This function removes user-specified proteins from a model_df object

Usage

rem_feature(model_df, rem_protein)

Arguments

model_df

A model_df object.

rem_protein

Name of the protein to remove.

Value

A model_df object.

Details

  • For example, you can choose to remove a protein from the model_df object if the protein does not show distinct patterns of variation among conditions. This protein may show mostly overlapping distributions in the feature plots.

  • Another incidence would be removing a protein that is very low in variable importance in the models built using train_models. You can visualize variable importance using varimp_plot.

See also

feature_plot, pre_process

Author

Chathurani Ranathunge

Examples


covid_model_df <- pre_process(fit_df = covid_fit_df, norm_df = covid_norm_df)
#> Total number of differentially expressed proteins (8) is less than n_top.
#> None of the proteins show high pair-wise correlation.
#> 
#> No highly correlated proteins to be removed.

## Remove sp|P22352|GPX3_HUMAN protein from the model_df object
covid_model_df1 <- rem_feature(covid_model_df, rem_protein = "sp|P22352|GPX3_HUMAN")
#> Protein sp|P22352|GPX3_HUMAN has been removed.