confIntExp {YAPSA} | R Documentation

## Compute confidence intervals

### Description

Compute confidence intervals using the (log-)likelihood ratio test, primarily for one input sample.

### Usage

    confIntExp(
      in_ind = 1,
      in_sigLevel = 0.05,
      in_delta = 1,
      in_exposure_vector = NULL,
      in_verbose = FALSE,
      ...
    )

### Arguments

`in_ind` | Index of the input signature to be variated.
`in_sigLevel` | Significance leve (one-sided)
`in_delta` | Inflation parameter for the alternative model.
`in_exposure_vector` | Exposure vector computed for the input sample.
`in_verbose` | Whether to run verbose (TRUE) or not (FALSE)
`...` | Input parameters passed on to variateExpSingle.

### Value

A list with entries

- `upper`: Upper bound of the confidence interval

- `lower`: Lower bound of the confidence interval

### Examples

     library(BSgenome.Hsapiens.UCSC.hg19)
     data(lymphoma_test)
     data(lymphoma_cohort_LCD_results)
     data(sigs)
     word_length <- 3
     temp_list <- create_mutation_catalogue_from_df(
       lymphoma_test_df,this_seqnames.field = "CHROM",
       this_start.field = "POS",this_end.field = "POS",
       this_PID.field = "PID",this_subgroup.field = "SUBGROUP",
       this_refGenome = BSgenome.Hsapiens.UCSC.hg19,
       this_wordLength = word_length)
     lymphoma_catalogue_df <- temp_list$matrix
     lymphoma_PIDs <- colnames(lymphoma_catalogue_df)
     data("lymphoma_cohort_LCD_results")
     lymphoma_exposures_df <-
       lymphoma_Nature2013_COSMIC_cutoff_exposures_df[, lymphoma_PIDs]
     lymphoma_sigs <- rownames(lymphoma_exposures_df)
     lymphoma_sig_df <- AlexCosmicValid_sig_df[, lymphoma_sigs]
     confIntExp(in_ind = 1, in_sigLevel = 0.05, in_delta = 0.4,
                in_exposure_vector = lymphoma_exposures_df[, 1],
                in_catalogue_vector = lymphoma_catalogue_df[, 1],
                in_sig_df = lymphoma_sig_df)

[Package YAPSA version 1.20.1 Index]