prepareC2 {EFMrep} | R Documentation |
prepareC is used in the functions contLikMLE to prepare input to C-call
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)
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. |
Assumes that all PH below threshold are removed. The function builds the data input to the C-code
ret A list of data input to call the C-code with
Oyvind Bleka