getStutterData: getStutterData

In oyvble/MPSproto: A Quantitative Model for MPS data with complex stutters

getStutterData

Description

helpfunction to obtain stutter data table used for making inference

Usage

getStutterData(
  dat,
  minStuttOccurence = 5,
  platform = "MPS",
  stutterTypes = NULL,
  verbose = FALSE
)

Arguments

dat	Datatable with columns (RefName,SampleName,Locus,Allele,Coverage,Dose)
minStuttOccurence	The number of required observations per stutter type (remaining put to noise)
platform	Platform type "MPS","CE". NOTE: CE has only consider only some stutter types (but also include -2bp)
stutterTypes	Stutter types. See getStutterTypeRule for supported types
verbose	Whether to print out progress

Details

Does not require getFilteredData first anymore The nomenlclature for stutters are as follows: BW1 means that the LUS motif is providing a backward stutter (n-1). FW1 means that the LUS motif is providing a forward stutter (n+1). BW2 means that the non-LUS motif is providing a backward stutter (n-1). etc... prefix "D" means double (n-2) n0 stutters are named as either FWBW or BWFW depending on which occuring first in the sequence (hence orientation matters!)

oyvble/MPSproto documentation built on March 19, 2024, 5:32 a.m.