qctree: CNVs QC Filtering Tree
In SinomeM/QCtreeCNV: Reducing the visual inspection effort in CNV calling

qctree

R Documentation

CNVs QC Filtering Tree

Description

The main functions of the QCtreeCNV package

Usage

qctree(
  cnvdt,
  cnvrs,
  loci,
  maxLRRSD = 0.35,
  maxBAFdrift = 0.01,
  maxGCWF = 0.02,
  minGCWF = -0.02,
  commonCNVRsMinFreq = NA,
  st2minov = 0.65,
  st4minlogr1 = -0.35,
  st4maxlogr1 = 0.4,
  st4maxBAFcDEL = 0.03,
  st4maxBAFcDUP = 0.125,
  st4maxBAFbDEL = 0.075,
  st5maxLRRSDlocus = 0.35,
  st5maxlogr1 = 0.5,
  st5maxBAFcDEL = 0.05,
  st5maxBAFcDUP = 0.15,
  st5maxBAFbDEL = 0.1,
  st5maxBAFbDUP = NA,
  clean_out = T,
  st5exclLRRSD = 0.65
)

Arguments

`cnvrs`	lorem ipsum
`loci`	lorem ipsum
`maxLRRSD`	lorem ipsum
`maxBAFdrift`	lorem ipsum
`maxGCWF`	lorem ipsum
`minGCWF`	lorem ipsum
`commonCNVRsMinFreq`	lorem ipsum
`st4minlogr1`	lorem ipsum
`st4maxlogr1`	lorem ipsum
`st4maxBAFcDEL`	lorem ipsum
`st4maxBAFcDUP`	lorem ipsum
`st4maxBAFbDEL`	lorem ipsum
`st5maxLRRSDlocus`	lorem ipsum
`st5maxBAFcDEL`	lorem ipsum
`st5maxBAFcDUP`	lorem ipsum
`st5maxBAFbDEL`	lorem ipsum
`st5maxBAFbDUP`	lorem ipsum
`clean_out`	lorem ipsum
`st5exclLRRSD`	lorem ipsum
`cnvs`	lorem ipsum
`qsdt`	lorem ipsum