Get demo data — get_demo • HandyCNV

The purpose of this function is to prepare demo data for 'HandyCNV'. The main reason is because of the SNP Signal Intensity and Genotype files always too large, when we making plots can select the data inside all CNVR regions instead of using the whole file. The output will extract all Signal Intensity, genotype and map information of given CNVRs. The new generated ped and map files keeps the same format with Plink Software, so we can --make-bed or --recode in Plink as well.

get_demo(
  intensity = NULL,
  ped = NULL,
  map = NULL,
  cnvr = NULL,
  freq_threshold = 0,
  folder = "demo_data"
)

Arguments

intensity	Four columns by order with
ped	Export from GenomeStudio
map	Export from GenomeStudio, requires four columns without header.
cnvr	Generate by 'call_cnvr', requires at least have four columns: Chr, Start, End, Frequency
freq_threshold	This used to filter the CNVRs, only prepare the demo data for CNVRs which passed this threshold
folder	Set name of new folder to save results

Value

Demo data of Intensity, Map, Ped file which appears only in CNVRs