Clean CNV — cnv_clean • HandyCNV

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

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.