The following error occurs when performing the stepwise QTL analysis:
No default penalty available for cross type bcsft
How do I build a model with cross type bcsft?
I looked it up, but I didn't understand.Thank you for your cooperation.
mapFunc<- "kosambi"
data<-read.cross("csvr", > file="Bc1F4.csv", estimate.map=T, >map.function=mapFunc, BC.gen=1, F.gen=4)
--Read the following data:
114 individuals
23 markers
73 phenotypes
-- Estimating generic map
-- Cross type: bcsft
data.sim<-sim.geno(data,step=5,>n.draws=128,map.function=mapFunc)
gr.sw<->stepwiseqtl(data.sim,pheno.col="gr",max.qtl=2)
Error in stepwiseqtl(data.sim, pheno.col="gr", max.qtl=2):
No default penalty available for cross type bcsft
I'm not familiar with the genomic analysis? field at all, so it's just a programming category (whether or not there are any errors):
As we cannot reproduce the code presented (there is no data referenced, there is something wrong with the syntax of R in the first place), we tried the following code supplemented by our imagination and finally got a similar error.
require(qtl)
mapFunc<- "kosambi"
datweb<-read.cross("csv", "https://rqtl.org/sampledata", "listeria.csv", estimate.map=T, map.function=mapFunc, BC.gen=T, F.gen=4)
data.sim<-sim.geno (dataweb, step=5, n.draws=128, map.function=mapFunc)
gr.sw<-stepwiseqtl(data.sim, pheno.col=1, max.qtl=2)
As stated in the error message, when I set the penalty, the error disappeared. However, I don't know about the QTL analysis, so I don't know if this value is appropriate.
gr.sw<-stepwiseqtl(data.sim,pheno.col=1,max.qtl=2,penalty=1:3)
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