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

In promor: Proteomics Data Analysis and Modeling Tools

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

Description

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.

Details

• After visualizing protein intensity variation among conditions with feature_plot or after assessing the importance of each protein in models using varimp_plot, you can choose to remove specific proteins (features) from the data frame.

• 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.

Value

A model_df object.

Author(s)

Chathurani Ranathunge

See Also

feature_plot, pre_process

Examples

covid_model_df <- pre_process(fit_df = covid_fit_df, norm_df = covid_norm_df)

## 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")

promor documentation built on July 26, 2023, 5:39 p.m.