comparison dartseq_seeduk_1c.R @ 22:12db48e80a98 draft

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21:5dab264e38c2

#Individuals with less than 60% missing values = 374 [99.5%]
#Individuals with less than 65% missing values = 375 [99.7%]
#[1] "Completed"
#
#
gl_call_rate <-  gl.filter.callrate(gl,method = 'loc', t=args[2])
#Reporting for a genlight object
#Note: Missing values most commonly arise from restriction site mutation.
#
#Initial no. of loci = 113138 
#  No. of loci deleted = 31509 

#  Call Rate > 0.75 
#  No. of loci: 81629 
#  No. of individuals: 376 
#  No. of populations:  0 
#
gl_rep <- gl.filter.repavg(gl_call_rate,t=args[3])
#Reporting for a genlight object
#Note: RepAvg is a DArT statistic reporting reproducibility averaged across alleles for each locus. 

#Initial no. of loci = 81629 
#No. of loci deleted = 6446 

#Individuals with less than 50% missing values = 373 [99.2%]
#Individuals with less than 55% missing values = 374 [99.5%]
#Individuals with less than 60% missing values = 375 [99.7%]
#[1] "Completed"

gl_final <-  gl.filter.callrate(gl_rep,method = 'ind', t=args[4])
#Reporting for a genlight object
#Note: Missing values most commonly arise from restriction site mutation.

#Initial no. of individuals = 376 
#Filtering a genlight object

22:12db48e80a98

#Individuals with less than 60% missing values = 374 [99.5%]
#Individuals with less than 65% missing values = 375 [99.7%]
#[1] "Completed"
#
#
gl_call_rate <-  gl.filter.callrate(gl,method = 'loc', t=as.double(args[2]))
#Reporting for a genlight object
#Note: Missing values most commonly arise from restriction site mutation.
#
#Initial no. of loci = 113138 
#  No. of loci deleted = 31509 

#  Call Rate > 0.75 
#  No. of loci: 81629 
#  No. of individuals: 376 
#  No. of populations:  0 
#
gl_rep <- gl.filter.repavg(gl_call_rate,t=as.double(args[3]))
#Reporting for a genlight object
#Note: RepAvg is a DArT statistic reporting reproducibility averaged across alleles for each locus. 

#Initial no. of loci = 81629 
#No. of loci deleted = 6446 

#Individuals with less than 50% missing values = 373 [99.2%]
#Individuals with less than 55% missing values = 374 [99.5%]
#Individuals with less than 60% missing values = 375 [99.7%]
#[1] "Completed"

gl_final <-  gl.filter.callrate(gl_rep,method = 'ind', t=as.double(args[4]))
#Reporting for a genlight object
#Note: Missing values most commonly arise from restriction site mutation.

#Initial no. of individuals = 376 
#Filtering a genlight object