max/ourMELONS
1
0
Fork 0
Code Issues 1 Pull requests Projects Releases Packages Wiki Activity Actions

Fixed docs

Browse source
This commit is contained in:
Waldir Leoncio 2023-09-11 13:13:55 +02:00
parent 882fcd4112
commit 70ec460106
5 changed files with 7 additions and 16 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

1
NAMESPACE
View file

@ -3,7 +3,6 @@
export(greedyMix) export(greedyMix)
export(handleData) export(handleData)
export(importFile) export(importFile)
export(load_fasta)
importFrom(R6,R6Class) importFrom(R6,R6Class)
importFrom(Rsamtools,scanBam) importFrom(Rsamtools,scanBam)
importFrom(adegenet,.readExt) importFrom(adegenet,.readExt)

4
R/greedyMix.R
View file

@ -3,11 +3,7 @@
#' @param format Data format. Format supported: "FASTA", "VCF" ,"BAM", "GenePop" #' @param format Data format. Format supported: "FASTA", "VCF" ,"BAM", "GenePop"
#' @param partitionCompare a list of partitions to compare #' @param partitionCompare a list of partitions to compare
#' @param ninds number of individuals #' @param ninds number of individuals
#' @param rowsFromInd a list of rows for each individual
#' @param noalle number of alleles
#' @param adjprior ajuster prior probabilities
#' @param npops number of populations #' @param npops number of populations
#' @param priorTerm prior terms
#' @param counts counts #' @param counts counts
#' @param sumcounts sumcounts #' @param sumcounts sumcounts
#' @param max_iter maximum number of iterations #' @param max_iter maximum number of iterations

5
R/load_fasta.R
View file

@ -5,16 +5,17 @@
#' #'
#' @param msa Either the location of a fasta file or ape DNAbin object containing the multiple sequence alignment data to be clustered #' @param msa Either the location of a fasta file or ape DNAbin object containing the multiple sequence alignment data to be clustered
#' @param keep_singletons A logical indicating whether to consider singleton mutations in calculating the clusters #' @param keep_singletons A logical indicating whether to consider singleton mutations in calculating the clusters
#' @param output_numbers A logical indicating whether to output the data as
#' numbers (TRUE) or letters (FALSE)
#' #'
#' @return A character matrix with filtered SNP data #' @return A character matrix with filtered SNP data
#' #'
#' @examples #' @examples
#' msa <- system.file("extdata", "seqs.fa", package = "rBAPS") #' msa <- system.file("extdata", "seqs.fa", package = "rBAPS")
#' snp.matrix <- load_fasta(msa) #' snp.matrix <- rBAPS:::load_fasta(msa)
#' @author Gerry Tonkin-Hill, Waldir Leoncio #' @author Gerry Tonkin-Hill, Waldir Leoncio
#' @seealso rhierbaps::load_fasta #' @seealso rhierbaps::load_fasta
#' @importFrom ape read.FASTA as.DNAbin #' @importFrom ape read.FASTA as.DNAbin
#' @export
load_fasta <- function(msa, keep_singletons = FALSE, output_numbers = TRUE) { load_fasta <- function(msa, keep_singletons = FALSE, output_numbers = TRUE) {
# Check inputs # Check inputs

8
man/greedyMix.Rd
View file

@ -46,14 +46,6 @@ greedyMix(
\item{fixedK}{if \code{TRUE}, the number of populations is fixed} \item{fixedK}{if \code{TRUE}, the number of populations is fixed}
\item{verbose}{if \code{TRUE}, prints extra output information} \item{verbose}{if \code{TRUE}, prints extra output information}
\item{rowsFromInd}{a list of rows for each individual}
\item{noalle}{number of alleles}
\item{adjprior}{ajuster prior probabilities}
\item{priorTerm}{prior terms}
} }
\description{ \description{
Clustering of individuals Clustering of individuals

5
man/load_fasta.Rd
View file

@ -10,6 +10,9 @@ load_fasta(msa, keep_singletons = FALSE, output_numbers = TRUE)
\item{msa}{Either the location of a fasta file or ape DNAbin object containing the multiple sequence alignment data to be clustered} \item{msa}{Either the location of a fasta file or ape DNAbin object containing the multiple sequence alignment data to be clustered}
\item{keep_singletons}{A logical indicating whether to consider singleton mutations in calculating the clusters} \item{keep_singletons}{A logical indicating whether to consider singleton mutations in calculating the clusters}
\item{output_numbers}{A logical indicating whether to output the data as
numbers (TRUE) or letters (FALSE)}
} }
\value{ \value{
A character matrix with filtered SNP data A character matrix with filtered SNP data
@ -20,7 +23,7 @@ running the hierBAPS algorithm.
} }
\examples{ \examples{
msa <- system.file("extdata", "seqs.fa", package = "rBAPS") msa <- system.file("extdata", "seqs.fa", package = "rBAPS")
snp.matrix <- load_fasta(msa) snp.matrix <- rBAPS:::load_fasta(msa)
} }
\seealso{ \seealso{
rhierbaps::load_fasta rhierbaps::load_fasta