prepareC2 {EFMrep}R Documentation

prepareC2

Description

prepareC is used in the functions contLikMLE to prepare input to C-call

Usage

prepareC2(dat, repNames, nC, condOrder = NULL, knownRef = NULL,
  kit = NULL, AT = 50, pC = 0.05, lambda = 0.01, fst = 0,
  incBS = FALSE, incFS = FALSE, knownRel = NULL, ibd = NULL)

Arguments

dat

A list which contains the output from function prepareData2 (samples,refs,freq)

repNames

Names of replicate samples

nC

Number of contributors in model (must be a consitant, same for all replicates)

condOrder

Specify conditioning references from refData (must be consistent order). For instance condOrder=(0,2,1,0) means that we restrict the model such that Ref2 and Ref3 are respectively conditioned as 2. contributor and 1. contributor in the model.

knownRef

Specify known non-contributing references from refData (indices). For instance knownRef=(1,2) means that reference 1 and 2 is known non-contributor in the hypothesis. This affectes coancestry correction.

kit

shortname of kit: Obtained from getKit().

AT

Analytical threshold. A vector per sample, or a list with marker elements per sample

pC

Dropin prob parameter. A vector per sample, or a list with marker elements per sample

lambda

DropinPH parameter. A vector per sample, or a list with marker elements per sample

fst

The co-ancestry coefficient. Default is 0. A vector per marker.

incBS

A boolean whether potential BW stutters are included

incFS

A boolean whether potential FW stutters are included

knownRel

Specify the index of the related contributing reference from refData (one index). For instance knownRel=2 means that unknown1 is related to reference 2 with ibd specified relationship.

ibd

the identical by decent coefficients list of the relationship for each unknowns (specifies the type of relationship). Default is NULL, meaning no related inds. Can be a list for each defined related pairs.

Details

Assumes that all PH below threshold are removed. The function builds the data input to the C-code

Value

ret A list of data input to call the C-code with

Author(s)

Oyvind Bleka


[Package EFMrep version 1.0.0 Index]