confidence_indel_only_calulation {YAPSA} | R Documentation

## Wrapper to compute confidence intervals for only INDEL signatures.

### Description

Wrapper function around `confIntExp`, which is applies to every signature or sample pair in a cohort. The extracted lower bound of the confidence intervals are added to the input data which is reodered and melted in order to prepare for visualization with ggplot2. The calculates of confidence intervals is based on a profiling likelihood algorithm and the wrapper calculates the data for the exposure contubution identefied with INDEL singature decomposition and the usage of `PCAWGValidID_absCutoffVector` data frame.

### Usage

    confidence_indel_only_calulation(in_current_indel_df)

### Arguments

`in_current_indel_df` | A INDEL mutational catalog. Mutational catalog can be constucted with `create_indel_mutation_catalogue_from_df`

### Details

The function makes use of differnet YAPSA functions. For each of the above stated cutoff vectors a per PID decompostion of the SNV and INDEL catalog is calulated respectivly using `LCD_complex_cutoff_perPID`. In a next step, `variateExp` which is a wrapper around `confIntExp` to compute confidenceintervals for a cohort is used. A dataframe is returend with the upper and lower bounds of the confidence intervals. In a last step `plotExposuresConfidence_indel` to plot the exposures to extracted signatures including confidence intervals computed with e.g. by `variateExp`.

### Value

A list is returned containing two object. First, the `p` gtable object which can be used for gaphically visualization, and second a dataframe containing the corrosponding upper and lower bounds of the confidence intervals.

### Examples

    data("GenomeOfNl_MutCat")
    temp_list <- confidence_indel_only_calulation(
                            in_current_indel_df=MutCat_indel_df)
    plot(temp_list$p_complete_PCAWG_ID)
    head(temp_list$complete_PCAWG_ID)

[Package YAPSA version 1.16.0 Index]