create_indel_mutation_catalogue_from_df {YAPSA} | R Documentation

## Wrapper to create an INDEL mutational catalog from a vlf-like data frame

### Description

From data frame constucted from a vcf-file file the function `create_indel_mutation_catalogue_from_df` creates a mutational catalog V by squencially applying the `attribute_sequence_contex_indel`, `attribute_sequence_contex_indel` and then `attribution_of_indels`. The runtime of the function is about 1 sec per 6 variants as sequence context as well as INDEL calssification are timeconsuming to compute (optimization ongoing)

### Usage

    create_indel_mutation_catalogue_from_df(
      in_dat,
      in_signature_df,
      in_REF.field = "REF",
      in_ALT.field = "ALT",
      in_verbose = FALSE
    )

### Arguments

`in_dat` | A data frame constructed from a vcf-like file of a whole cohort or single-sample. The first columns are those of a standard vcf file (`CHROM`, `POS`, `REF` and `ALT`), followed by an arbitrary number of custom or used defined columns. One of these can carry a PID (patient or sample identifyier) and one can carry subgroup information.
`in_signature_df` | A numeric data frame `W` with `n` rows and `l` columns, n being the number of features and l being the number od signatures. Data frame containing INDEL signatures which should be used to create the mutational cataologe `V`.
`in_REF.field` | String indicating which column of `in_dat` carries the reference base if dealing with data frames
`in_ALT.field` | String indicating which column of `in_dat` carries the variant base if dealing with data frames
`in_verbose` | Verbose if `in_verbose=1`

### Value

A dataframe in the format of a mutational catalog `V`, which can be used for `LCD` analysis

### Examples

    data(sigs_pcawg)
    data(GenomeOfNl_raw)
    temp_df <- translate_to_hg19(GenomeOfNl_raw[1:200,],"CHROM")
    temp_df$PID <- sample(c("PID1","PID2","PID3","PID4","PID5"),200,replace=TRUE)
    temp <- create_indel_mutation_catalogue_from_df(in_dat = temp_df,
       in_signature_df = PCAWG_SP_ID_sigs_df,
       in_REF.field = "REF",
       in_ALT.field = "ALT",
       in_verbose = FALSE)
    dim(temp)
    head(temp)

[Package YAPSA version 1.16.0 Index]