In c5sire/licor: Tools for processing molecular data from a Licor sequencer

library(licor, quietly=TRUE, verbose=FALSE)
library(stringr)
if(is.null(data)){
  #fn = "../files/out1.xlsx"
  #wb = loadWorkbook(fn)
  #data = readWorksheet(wb,"Joined Licor data")
  #smry = readWorksheet(wb,"Summary Licor data")
} else {
  fn = basename(data$filename)
  smry = summary.licor(data)
  data = join.markers(data)
}
nal = ncol(data)-1 # Number of alleles

Licor marker report for file: r fn

There were r nrow(data) samples in the joined marker matrix. The matrix has a total of r nal alleles across a total of r nrow(smry) markers.

Summary of the marker data in the original file:

library(xtable) 
print(xtable(smry), type='html') 

Duplicated individuals across all alleles

mprof = apply(data[,2:ncol(data)],1,paste,collapse="")
ndups = length(which(duplicated(mprof)))
ndpct = round((ndups/nrow(data)*100), 0)
gdups = data$Genotype[duplicated(mprof)]

There are r ndups (r ndpct)% duplicated genotypes (having exactly the same molecular profile). They are (omitting the first occurence):

r paste(gdups, collapse=', ').

out = NULL
fcn = "../reports/child.Rmd"
for(x in 1:nrow(smry)){
  out = c(out,knit_child(fcn))
}

r paste(out, collapse = "\n")

c5sire/licor documentation built on May 13, 2019, 10:35 a.m.