Ajoute un example de debut de fichier genotype.R

NAMESPACE

@@ -5,6 +5,10 @@ export(error_jc)
 export(log_add_exp)
 export(log_diff_exp)
 export(log_sum_exp)
+export(pdata_genotype)
+export(pnuc_genotype)
+export(pnuc_hetero_genotype)
+export(pnuc_homo_genotype)
 export(sequencing_error)
 export(simulate_sites)
 import(dplyr)

R/genotype.R

+#' Compute probabilty of data knowing the genotype.
+#' 
+#' @param obs.a the number of observed `A`
+#' @param obs.c the number of observed `C`
+#' @param obs.g the number of observed `G`
+#' @param obs.t the number of observed `T`
+#' @param haplotype.1 a character indicating the first haplotype
+#'                    (A, C, G, ou T)
+#' @param haplotype.2 a character indicating the second haplotype
+#'                    (A, C, G, ou T)
+#' @param sequencing.error a numeric ranging betweing 0 and 1
+#'                    indicating the sequencing error rate                   
+#' 
+#' @return returns the log of the probality of the data 
+#'         knowning the genotype.
+#'         
+#' @examples 
+#'     pdata_genotype(4,3,0,1,'A','C',0.01)
+#'     
+#' @export
+pdata_genotype = function(obs.a,obs.c,obs.g,obs.t,
+                          haplotype.1,haplotype.2,
+                          sequencing.error) {
+  
+}
+
+#' Compute probability of nucleotide observation knowning genotype.
+#' 
+#' @param haplotype.1 a character indicating the first haplotype
+#'                    (A, C, G, ou T)
+#' @param haplotype.2 a character indicating the second haplotype
+#'                    (A, C, G, ou T)
+#' @param sequencing.error a numeric ranging betweing 0 and 1
+#'                    indicating the sequencing error rate                   
+#' 
+#' @return a vector of four probabilities for A, C, G and T 
+#'         observations
+#'
+#' @examples 
+#'   pnuc_genotype("A","T",0.01)
+#'   
+#' @export
+pnuc_genotype = function(haplotype.1,haplotype.2,
+              sequencing.error) {
+  
+  if (haplotype.1 == haplotype.2)
+    rep = pnuc_homo_genotype(haplotype.1,sequencing.error)
+  else
+    rep = pnuc_hetero_genotype(haplotype.1,
+                               haplotype.2,
+                               sequencing.error)
+  
+  return(rep)
+}
+
+#' Compute probability of nucleotide observation 
+#' knowning an heterozygote genotype.
+#' 
+#' @param haplotype.1 a character indicating the first haplotype
+#'                    (A, C, G, ou T)
+#' @param haplotype.2 a character indicating the second haplotype
+#'                    (A, C, G, ou T)
+#' @param sequencing.error a numeric ranging betweing 0 and 1
+#'                    indicating the sequencing error rate                   
+#' 
+#' @return a vector of four probabilities for A, C, G and T 
+#'         observations
+#'
+#' @examples 
+#'   pnuc_hetero_genotype("A","T",0.01)
+#'   
+#' @export
+pnuc_hetero_genotype = function(haplotype.1,haplotype.2,
+              sequencing.error) {
+  pnuc = rep(sequencing.error/6*5,4)
+  names(pnuc)=c("A","C","G","T")
+  pnuc[haplotype.1] = 0.5 - sequencing.error/6*5
+  pnuc[haplotype.2] = pnuc[haplotype.1]
+  
+  return(pnuc)
+  
+}
+
+#' Compute probability of nucleotide observation 
+#' knowning an homozygote genotype.
+#' 
+#' @param haplotype   a character indicating the first haplotype
+#'                    (A, C, G, ou T)
+#' @param sequencing.error a numeric ranging betweing 0 and 1
+#'                    indicating the sequencing error rate                   
+#' 
+#' @return a vector of four probabilities for A, C, G and T 
+#'         observations
+#'
+#' @examples 
+#'   pnuc_hetero_genotype("A","T",0.01)
+#'   
+#' @export
+pnuc_homo_genotype = function(haplotype,
+              sequencing.error) {
+  
+  pnuc = rep(sequencing.error/3,4)
+  names(pnuc)=c("A","C","G","T")
+  pnuc[haplotype] = 1 - sequencing.error
+  
+  return(pnuc)
+}

man/pdata_genotype.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/genotype.R
+\name{pdata_genotype}
+\alias{pdata_genotype}
+\title{Compute probabilty of data knowing the genotype.}
+\usage{
+pdata_genotype(obs.a, obs.c, obs.g, obs.t, haplotype.1, haplotype.2,
+  sequencing.error)
+}
+\arguments{
+\item{obs.a}{the number of observed `A`}
+
+\item{obs.c}{the number of observed `C`}
+
+\item{obs.g}{the number of observed `G`}
+
+\item{obs.t}{the number of observed `T`}
+
+\item{haplotype.1}{a character indicating the first haplotype
+(A, C, G, ou T)}
+
+\item{haplotype.2}{a character indicating the second haplotype
+(A, C, G, ou T)}
+
+\item{sequencing.error}{a numeric ranging betweing 0 and 1
+indicating the sequencing error rate}
+}
+\value{
+returns the log of the probality of the data 
+        knowning the genotype.
+}
+\description{
+Compute probabilty of data knowing the genotype.
+}
+\examples{
+    pdata_genotype(4,3,0,1,'A','C',0.01)
+    
+}

man/pnuc_genotype.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/genotype.R
+\name{pnuc_genotype}
+\alias{pnuc_genotype}
+\title{Compute probability of nucleotide observation knowning genotype.}
+\usage{
+pnuc_genotype(haplotype.1, haplotype.2, sequencing.error)
+}
+\arguments{
+\item{haplotype.1}{a character indicating the first haplotype
+(A, C, G, ou T)}
+
+\item{haplotype.2}{a character indicating the second haplotype
+(A, C, G, ou T)}
+
+\item{sequencing.error}{a numeric ranging betweing 0 and 1
+indicating the sequencing error rate}
+}
+\value{
+a vector of four probabilities for A, C, G and T 
+        observations
+}
+\description{
+Compute probability of nucleotide observation knowning genotype.
+}
+\examples{
+  pnuc_genotype("A","T",0.01)
+  
+}

man/pnuc_hetero_genotype.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/genotype.R
+\name{pnuc_hetero_genotype}
+\alias{pnuc_hetero_genotype}
+\title{Compute probability of nucleotide observation 
+knowning an heterozygote genotype.}
+\usage{
+pnuc_hetero_genotype(haplotype.1, haplotype.2, sequencing.error)
+}
+\arguments{
+\item{haplotype.1}{a character indicating the first haplotype
+(A, C, G, ou T)}
+
+\item{haplotype.2}{a character indicating the second haplotype
+(A, C, G, ou T)}
+
+\item{sequencing.error}{a numeric ranging betweing 0 and 1
+indicating the sequencing error rate}
+}
+\value{
+a vector of four probabilities for A, C, G and T 
+        observations
+}
+\description{
+Compute probability of nucleotide observation 
+knowning an heterozygote genotype.
+}
+\examples{
+  pnuc_hetero_genotype("A","T",0.01)
+  
+}

man/pnuc_homo_genotype.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/genotype.R
+\name{pnuc_homo_genotype}
+\alias{pnuc_homo_genotype}
+\title{Compute probability of nucleotide observation 
+knowning an homozygote genotype.}
+\usage{
+pnuc_homo_genotype(haplotype, sequencing.error)
+}
+\arguments{
+\item{haplotype}{a character indicating the first haplotype
+(A, C, G, ou T)}
+
+\item{sequencing.error}{a numeric ranging betweing 0 and 1
+indicating the sequencing error rate}
+}
+\value{
+a vector of four probabilities for A, C, G and T 
+        observations
+}
+\description{
+Compute probability of nucleotide observation 
+knowning an homozygote genotype.
+}
+\examples{
+  pnuc_hetero_genotype("A","T",0.01)
+  
+}