expectedValues: Calculate expected values

In daynefiler/filer2020B: Analysis for DOI to be added

Description

Collection of functions for calculating various expected values

Usage

cfExpPMAR(ffVec, seqError = 0.003, clpsList = TRUE)

cfExpSdPMAR(ffVec, dep, seqError = 0.003, clpsList = TRUE)

cfExpUnqHet(qVec)

cfExpGenoFreq(qVec, clpsList = TRUE)

Arguments

ffVec	Numeric, fetal fractions
clpsList	List items will be collapsed to a vector when possible
dep	Integer of length 1, total read depth
qVec	Numeric, minor allele frequencies

Details

Default seqError of 0.003 taken from PMID30026539 (mean + 1SD to over- estimate).

Functions

• cfExpPMAR: Expected proportion of minor allele reads

• cfExpSdPMAR: Expected standard deviation on proportion of minor allele reads

• cfExpUnqHet: Expected proportion of sites with unique fetal alleles

• cfExpGenoFreq: Expected proportion of genotype pairs

daynefiler/filer2020B documentation built on Dec. 30, 2021, 8:44 a.m.