confidence_indel_calulation {YAPSA} | R Documentation

## Wrapper to compute confidence intervals for SNV and INDEL signatures of a cohort or single-sample

### 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 SNV and INDEL signature decompositions and application of the following cutoffs:

1. `CosmicValid_absCutoffVector`

2. `CosmicValid_normCutoffVector`

3. `CosmicArtif_absCutoffVector`

4. `CosmicArtif_normCutoffVector`

5. `PCAWGValidSNV_absCutoffVector`

6. `PCAWGValidID_absCutoffVector`

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` wich is a wrapper around `confIntExp` to compute confidence intervals 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`.

### Usage

    confidence_indel_calulation(in_current_indel_df, in_current_snv_df)

### Arguments

`in_current_indel_df` | A INDEL mutational catalog. Mutational catalog can be constucted with `create_indel_mutation_catalogue_from_df`
`in_current_snv_df` | A SNV mutational catalog. Mutational catalog can be constuced with `create_mutation_catalogue_from_df`

### Value

A list is returned containing 12 objects. For each cutoff data frame two corrosponding object are present. 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")

[Package YAPSA version 1.16.0 Index]