call_cnv | R Documentation |
Call Copy-number Variation from SLRatio and segmentation
call_cnv(
sample_segmentation,
sample_zscore,
callChr = seq_len(22),
tfs = c(0, 0.7),
ploidies = c(1.5, 3),
MaxCN = 4
)
sample_segmentation |
segmentation dataframe from segmentByPSCBS |
sample_zscore |
zscore dataframe |
callChr |
chromosome to analysis : Default c(1:22) |
tfs |
range of fitting tumor fraction : Default c(0,0.8) |
ploidies |
range of fitting chromosomal ploidy : Default c(1.5,4) |
MaxCN |
maximum copy-number : Default 4 |
List of cnvcalling solutions
### Loading example SampleBam file
example_file <- system.file("extdata","example_patientcfDNA_SampleBam.RDS",package = "cfdnakit")
sample_bambin <- readRDS(example_file)
### Example PoN
PoN_rdsfile <- system.file("extdata","ex.PoN.rds",package = "cfdnakit")
pon_profiles <- readRDS(PoN_rdsfile)
sample_profile <- get_fragment_profile(sample_bambin,sample_id = "Patient1")
sample_zscore <- get_zscore_profile(sample_profile,pon_profiles)
sample_zscore_segment <- segmentByPSCB(sample_zscore)
sample_cnv <- call_cnv(sample_zscore_segment,sample_zscore, tfs=c(0.1,0.3),ploidies=c(1.5,2), MaxCN=3)
plot_cnv_solution(sample_cnv,selected_solution = 1)
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