inter_res_merge: Combine the results from multiple methods in a single object

In SinomeM/CNVgears: A Framework to Combine, Analize and Interpret CNVs Calling Results

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)

SinomeM/CNVgears documentation built on Nov. 21, 2021, 5:34 a.m.