relMix: Relationship Inference for DNA Mixtures

## ----eval=FALSE---------------------------------------------------------------
#  relMixGUI()

## ----out.width =  "100%", fig.retina = NULL,echo=FALSE,fig.cap="Figure 1: The RelMix main window."----
knitr::include_graphics("relMix_screenshot.png")

## ----echo=FALSE, results='asis'-----------------------------------------------
M <- read.table("mixture.txt",sep="\t",header=TRUE)
requireNamespace("pander",quietly=TRUE)
pander::pandoc.table(rbind(head(M, 5),data.frame(SampleName='...',Marker='...',Allele1='...',Allele2='...',Allele3='...')),missing="",caption="Table 1: The mixture profile in example 1.")

## ----echo=FALSE, results='asis'-----------------------------------------------
G <- read.table("references.txt",sep="\t",header=TRUE)
G2 <- rbind(G[1:2,],data.frame(SampleName='...',Marker='...',Allele1='...',Allele2='...'),G[22:24,],data.frame(SampleName='...',Marker='...',Allele1='...',Allele2='...'),G[44,])
rownames(G2) <- NULL
knitr::kable(G2,caption="Table 2: Reference profiles for mother and alleged father in example 1.")

## ----fig.align='center', echo=FALSE, fig.cap='Figure 2: Database window.'-----
knitr::include_graphics("database_crop.png",dpi=80)

## ----echo=FALSE, results='asis'-----------------------------------------------
freqs <- read.table("frequencies22Markers.txt",sep="\t",header=T,stringsAsFactors=F)
freqs2 <- freqs[11:18,1:5]
rownames(freqs2) <- NULL
pander::pandoc.table(cbind(rbind(freqs2,rep('...',5)),'...'=rep('...',9)),missing="",digits=4,caption="Table 3: Excerpt of the allele frequency database in example 1. Dots are used as decimal separator.")

## ----out.width =  "50%", fig.retina = NULL,echo=FALSE,fig.cap="Figure 3: Database options. Theta value, silent allele frequency and minimum allele frequency."----
knitr::include_graphics("database_options.png")

## ----out.width =  "60%", fig.retina = NULL,echo=FALSE,fig.cap="Figure 4: Define the pedigrees in example 1."----
knitr::include_graphics("pedigrees_ex1.png")

## ----out.width =  "50%", fig.retina = NULL,echo=FALSE,fig.cap="Figure 5: Specify mother and child as the contributors in both pedigrees in example 1."----
knitr::include_graphics("contributors_ex1.png")

## ----out.width =  "50%", fig.retina = NULL,echo=FALSE,fig.cap="Figure 6: In example 1 we assume dropout probabilities 0 for the mother and 0.1 for the child and drop-in 0.05."----
knitr::include_graphics("dropout_ex1.png")

## ----out.width="100%",, fig.retina = NULL,echo=FALSE,fig.cap="Figure 7: Results for example 1."----
knitr::include_graphics("results_ex1.png")

## ----echo=FALSE, results='asis'-----------------------------------------------
M <- read.table("mixture_silent_ex.txt",sep="\t",header=TRUE)
pander::pandoc.table(head(M, 5),missing="",caption="Table 4: Mixture file for example 2.")

## ----echo=FALSE, results='asis'-----------------------------------------------
G <- read.table("references_silent.txt",sep="\t",header=TRUE)
rownames(G) <- NULL
knitr::kable(G,caption="Table 5: Reference profile for the known contributor (C1) in example 2.")

## ----echo=FALSE, results='asis'-----------------------------------------------
freqs <- read.table("freqsSilent.txt",sep="\t",header=T,stringsAsFactors=F)
rownames(freqs) <- NULL
pander::pandoc.table(freqs,missing="",digits=4,caption="Table 6: Allele frequencies.")

## ----out.width =  "50%", fig.retina = NULL,echo=FALSE,fig.cap="Figure 8: Database options for example 2."----
knitr::include_graphics("database_options_ex2.png")

## ----out.width =  "50%", fig.retina = NULL,echo=FALSE,fig.cap="Figure 9: Scale frequencies or add rest allele."----
knitr::include_graphics("scaling_ex2.png")

## ----out.width =  "50%", fig.retina = NULL,echo=FALSE,fig.cap="Figure 10: Mutations in example 2."----
knitr::include_graphics("mutations_ex2.png")

## ----echo=FALSE, results='asis'-----------------------------------------------
M <- read.table("custom_pedigree_maternity_duo.ped",sep="\t",header=TRUE, stringsAsFactors=FALSE)
requireNamespace("pander",quietly=TRUE)
pander::pandoc.table(M,caption="Table 7: The ped file specifying the mother-child pedigree in example 2.")

## ----echo=FALSE, results='asis'-----------------------------------------------
M <- read.table("custom_pedigree_unrelated_duo.ped",sep="\t",header=TRUE, stringsAsFactors=FALSE)
requireNamespace("pander",quietly=TRUE)
pander::pandoc.table(M,caption="Table 8: The ped file specifying that the two contributors in example 2 are unrelated.")

## ----out.width =  "60%", fig.retina = NULL,echo=FALSE,fig.cap="Figure 11: We import custom pedigrees from R scripts in example 2."----
knitr::include_graphics("custom_ped_ex2.png")

## ----out.width =  "50%", fig.retina = NULL,echo=FALSE,fig.cap="Figure 12: Tick both individuals as contributors to the mixture in both pedigrees."----
knitr::include_graphics("contributors_ex2.png")

## ----out.width =  "40%", fig.retina = NULL,echo=FALSE,fig.cap="Figure 13: Possible dropout for both contributors in example 2."----
knitr::include_graphics("dropout_ex2.png")

## ----out.width =  "100%", fig.retina = NULL,echo=FALSE,fig.cap="Figure 14: Computed LR for example 2."----
knitr::include_graphics("results_ex2.png")