cnv_clean: Clean CNV

In JH-Zhou/HandyCNV: HandyCNV: An R package for Standardized Summary, Annotation, Comparison, and Visualization of CNV, CNVR and ROH

Description

Import CNV call results produced by the software packages PennCNV and CNVPartition, and converts them into a standard format for use in other functions in the 'HandyCNV' package. It now support to accept a CNV list in the standard format, the standard format should have at least five columns with header: Sample_ID, Chr, Start, End, CNV_Value

Usage

cnv_clean(
  cnvpartition = NULL,
  penncnv = NULL,
  standard_cnv = NULL,
  drop_length = 5,
  penn_id_sep = "cnv/",
  folder = "cnv_clean"
)

Arguments

cnvpartition	load CNV results from CNVPartition
penncnv	load CNV results from PennCNV
standard_cnv	Load a user-generated CNV input file. The following columns must be present: Sample_ID, Chr, Start, End, CNV_Value
drop_length	exclude CNVs longer than this threshold, unit is "Mb"
penn_id_sep	the separator in the 'Sample ID' column of PennCNV results. Useful if the ID is bound to the path
folder	set the name of the output folder

Value

Formatted CNV results and brief summary files.

JH-Zhou/HandyCNV documentation built on Dec. 18, 2021, 12:25 a.m.