Nothing
## ----setup, echo=FALSE---------------------------------------------------
knitr::opts_chunk$set(tidy = TRUE,
fig.align = 'center', fig.width = 8, fig.height = 6)
## ----admix-read----------------------------------------------------------
library(starmie)
# get Q and P files for K = 3
p3 <- system.file("extdata/hapmap3_files", "hapmap3.3.P", package = "starmie")
q3 <- system.file("extdata/hapmap3_files", "hapmap3.3.Q", package = "starmie")
k3_admix <- loadAdmixture(q3, p3)
k3_admix
## ----admix-log-----------------------------------------------------------
k3_log <- system.file("extdata/hapmap3_files", "log3.out", package = "starmie")
k3_admix <- loadAdmixture(q3, p3, k3_log)
k3_admix
## ----admix-object, echo=FALSE--------------------------------------------
list_names <- names(k3_admix)
list_description <- c("K parameter supplied to ADMIXTURE",
"Number of samples",
"Number of markers",
"Individual ancestral probability of membership to cluster",
"Estimated ancestral allele frequencies for each cluster",
"Model fit statistics")
knitr::kable(data.frame(attributes = list_names,
description = list_description))
## ----plotbar-------------------------------------------------------------
plotBar(k3_admix)
## ----plotbar2------------------------------------------------------------
plotBar(k3_admix, facet = FALSE)
## ----multirun------------------------------------------------------------
admix_multi <- exampleAdmixture()
admix_multi
## ------------------------------------------------------------------------
bestK(admix_multi)
## ------------------------------------------------------------------------
sessionInfo()
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