CliP is an algorithm for clonal structure identification through penalizing pairwise differences by Wenyi Wang Lab at MD Anderson Cancer Center in Houston.
Usage
to_clip(
cd,
out_dir = NULL,
snvs_name = default_SNVs(cd),
cnvs_name = default_CNVs(cd),
purity_column = "purity",
keep_chromosomes = str_c("chr", 1:22)
)Arguments
- cd
cevodata object
- out_dir
Directory where to save files. List of items is returned if out_dir is NULL
- snvs_name
name of the snvs to use
- cnvs_name
name of the cnvs to use
- purity_column
name of the metadata column with the purity estimates to be used
- keep_chromosomes
list of non-sex chromosomes. CliP does not use sex chromosomes