inter_res_merge {CNVgears} | R Documentation

## Combine the results from multiple methods in a single object

### Description

`inter_res_merge` combines the results of multiple CNV calling methods imported via `read_results` into a single `CNVresults` object.

### Usage

    inter_res_merge(
      res_list,
      sample_list,
      chr_arms,
      prop = 0.3,
      inner_outer = "outer"
    )

### Arguments

`res_list` | a `list` of `CNVresults`.
`sample_list` | cohort information
`chr_arms` | a `data.table` containing chromosomal arms locations. They are bundled in the package for hg18, hg19 and hg38 (`hgXX_chr_arms`).
`prop` | proportion of reciprocal overlap to define two calls as "replicated".
`inner_outer` | keep "inner" or "outer" borders? If NA all columns will be kept.

### Details

Multiple `CNVresults` objects are combined into a single object and replicated calls are merged. The amount of reciprocal overlap necessary to define two calls as "replicated" is controlled with the `prop` parameter. When merging two or more events there will be two borders, inner and outer. By default the outer border are kept as "start" and "end" of the final table. If the user want to keep all the information `inner_outer` can be set to NA. In this case "start" and "end" will also be the outer borders. This is done because a `CNVresults` object need explicit "start" and "end" columns.

### Value

a `CNVresults` containing the merge of the one provided via `res_list`.

### Examples

    DT <- inter_res_merge(res_list = list(penn_22, quanti_22),
    sample_list= cohort_examples, chr_arms= hg19_chr_arms)

[Package CNVgears version 1.0.0 Index]