error_jc.Rd 1.18 KB
 Eric Coissac committed Oct 19, 2018 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 % Generated by roxygen2: do not edit by hand % Please edit documentation in R/simulate.R \name{error_jc} \alias{error_jc} \title{Build error matrix.} \usage{ error_jc(rate) } \arguments{ \item{rate}{is the global error probability per site expressed as a numeric value ranging between 0 and 1.} } \value{ a 4 x 4 numeric matrix providing sequencing error probalibiltie for each nucleotides. } \description{ Error matrix is a 4 x 4 numeric matrix providing sequencing error probalibiltie for each nucleotides. Each row correspond to one of the four nucleotides A,C,G,T. Each column indicates the probability of reading a given nucleotide considering that the TRUE one is indicated by the row. error.jc build an error matrix following the Juke et Cantor model where all errors are equiprobable. } \examples{ # Build an error matrix corresponding # to 5\% of sequencing error err = error_jc(0.05) err # A C G T # A 0.95000000 0.01666667 0.01666667 0.01666667 # C 0.01666667 0.95000000 0.01666667 0.01666667 # G 0.01666667 0.01666667 0.95000000 0.01666667 # T 0.01666667 0.01666667 0.01666667 0.95000000 } \author{ Eric Coissac }