Run_Genotyping {GenoTriplo}

Launch genotyping phase in parallel

Description

Function that launch the genotyping phase from the dataset with SampleName, Contrast and SigStren for each markers and the result of the 'Run_clustering' function.

Usage

Run_Genotyping(
  data_clustering,
  res_clust,
  ploidy,
  SeuilNoCall = 0.85,
  SeuilNbSD = 2.8,
  SeuilSD = 0.28,
  n_core = 1,
  corres_ATCG = NULL,
  pop = "Yes",
  cr_marker = 0.97,
  fld_marker = 3.4,
  hetso_marker = -0.3,
  save_n = "",
  batch = "",
  ALL = TRUE,
  path_log = ""
)

Arguments

data_clustering

dataframe result from create dataset phase

res_clust

object from clustering phase

ploidy

ploidy of offspring

SeuilNoCall

threshold of the probability of belonging to a cluster

SeuilNbSD

threshold for the distance between an individuals and his cluster (x=Contrast)

SeuilSD

threshold for the standard deviation of a cluster (SeuilSD*(1+0.5*abs(mean_contrast_cluster)))

n_core

number of cores used for parallelization

corres_ATCG

dataframe with the correspondence between A/B of AXAS and A/T/C/G (three columns : probeset_id, Allele_A, Allele_B)

pop

Yes or No : are individuals from a same population

cr_marker

call rate threshold

fld_marker

FLD threshold

hetso_marker

HetSO threshold

save_n

name of the saving file. If ” no auto save and return value is changed

batch

batch number in case of parallelization else ignore

ALL

TRUE/FALSE whether the dataset has been cut or not (from the shiny app)

path_log

path for log file when run by the shiny app

Value

if save_n != ” : 3 objects list : dataframe with call rate by individuals, dataframe with call rate and other metrics of markers and another dataframe – Automatically save results. Else : return list with genotype

Examples

data(GenoTriplo_to_clust)
data(GenoTriplo_to_geno)
res = Run_Genotyping(data_clustering=GenoTriplo_to_clust,
                     res_clust=GenoTriplo_to_geno,
                     ploidy=3)