processInput: Preprocessing function
In cecileane/WGDgc: Whole genome duplication detection using gene counts

Description Usage Arguments Details Value Examples

View source: R/processInput.R

Checking arguments and preparing data for future optimization

1 2	processInput(tr, equalBDrates=FALSE, fixedRetentionRates=TRUE, startingBDrates=c(0.01, 0.02),startingQ=NULL)

`tr`	a species tree in SIMMAP format (see Details of function MLEGeneCount).
`equalBDrates`	if `TRUE`, the duplication and loss rates are equal.
`fixedRetentionRates`	if `TRUE`, retention rates will be fixed to `startingQ` during the future optimization. If `FALSE`, retention rates will be considered as parameters and will be estimated by maximum likelihood.
`startingBDrates`	Vector of size 2 as starting values for the duplication and loss rates. When `equalBDrates=TRUE` only the first component is used.
`startingQ`	Vector of starting values for retention rates. Default is 0.5 for all WGD events.

The vector para of starting values for the parameters to be optimized is of size 1+number of WGDs if the birth and death rates are assumed equal, or 2+number of WGDs otherwise. It starts with log(StartingBDrates[1]) if equalBDrates is TRUE, with log(StartingBDrates) otherwise, and the remaining components (corresponding to the retention rates) are startingQ if startingQ is provided, 0.5 otherwise.

For WGT events, the 2 extra copies are assumed to be retained independently. With retention rate q, the probability to retain all 3 gene copies is then q^2, the probability to retain 2 gene copies is 2*q*(1-q), and the probability to retain the original gene only is (1-q)^2.

lower and upper are vectors whose sizes correspond to the number of parameters for the lower and upper bounds of the different parameters in a subsequent optimization search. The log of the duplication and loss rates are unconstrained, while duplicate retention rates are constrained in [0,1].

`phyloMat`	data frame to represent the phylogeny. The number of rows is the number of nodes in the species tree. There are 5 columns (Parent, Child, Time, Species, type).
`nLeaf`	number of present-day species (i.e. number of leaves)
`nNode`	number of nodes in the species tree
`wgdTab`	data frame with 5 columns. Each row corresponds to a WGD(s) or WGT(s). The first column gives the node just before the WGD/T. The second column 'type' says if the event is a WGD or WGT. The remaining columns contain the probabilities that only the original gene is retained, or if 2 (or 3) gene copies are retained.
`para`	Vector of parameters to be optimized. see Details
`lower`	Lower bounds for later optimization. see Details
`upper`	Upper bounds for later optimization. see Details

tre.string = "(D:{0,18.03},(C:{0,12.06},(B:{0,7.06},
              A:{0,7.06}):{0,2.49:wgd,0:0,2.50}):{0, 5.97});"
tre.phylo4d = read.simmap(text=tre.string)
processInput(tre.phylo4d)