variateExpSingle {YAPSA} | R Documentation

## Wrapper for the likelihood ratio test

### Description

Application of the likelihood ratio test to mutational signatures, primarily for one single sample.

### Usage

    variateExpSingle(
      in_catalogue_vector,
      in_sig_df,
      in_exposure_vector,
      in_ind,
      in_factor = 1,
      in_pdf = NULL,
      verbose = FALSE
    )

### Arguments

`in_catalogue_vector` | Mutational catalog of the input sample.
`in_sig_df` | Data frame encoding the signatures used for the analysis.
`in_exposure_vector` | Exposure vector computed for the input sample.
`in_ind` | Index specifying which signature among `in_sig_df` is to be tested.
`in_factor` | Deviation factor of the altered alternative model.
`in_pdf` | Probability distibution function, parameter passed on to logLikelihood and later to computeLogLik
`verbose` | Verbose if `in_verbose=1`

### Value

Returns a list

### 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]
     variateExpSingle(
       in_ind = 1,
       in_factor = 1.5,
       in_catalogue_vector = lymphoma_catalogue_df[, 1],
       in_sig_df = lymphoma_sig_df,
       in_exposure_vector = lymphoma_exposures_df[, 1])

[Package YAPSA version 1.16.0 Index]