rami1
February 10, 2022, 3:37pm
1
I have tried to use asmap package it for a RIL population of wheat (no heterozygous alleles) to construct the map. I have an error “Error in mstmap.data.frame(rils, pop.type = "ARIL", dist.fun = "kosambi", :
MSTMC <- mstmap.data.frame(rils, pop.type = "ARIL", dist.fun = "kosambi", objective.fun = "COUNT", p.value = asmpvalue, noMap.dist = 15, noMap.size = 0, miss.thresh = 10, mvest.bc = TRUE , trace = FALSE , as.cross = FALSE)
Hi, welcome!
We don't really have enough info to help you out. Could you ask this with a minimal REPR oducible EX ample (reprex)
Here's a discussion on setting up data for a reprex
make it run - include the minimal code required to reproduce your error on the data…
The error message also notes
Non-allowable allele encodings in DH marker set”
Which seems to be hinting at a likely source of the problem.
rami1
February 10, 2022, 6:10pm
3
Thanks for your reply. actually I am trying to construct the genetic map with a set of SNP markers and I use the ASMap package and adapting their package to my data the data loading was fine and my script from beginning is as below
library(ASMap)
> poptype='RIL5'
> ASMpvalue=1e-6
> mstMC <- mstmap.data.frame(data, pop.type = poptype, dist.fun = "kosambi",objective.fun = "COUNT", p.value = ASMpvalue, noMap.dist = 30, noMap.size = 2,miss.thresh = 10, mvest.bc = FALSE, traces=TRUE,as.cross=TRUE)
Error in mstmap.data.frame(data, pop.type = poptype, dist.fun = "kosambi", :
Non-allowable allele encodings in RIL marker set
The few columns of data is as below
Marker
101A
101B
101C
101D
101E
101F
101G
101H
102A
102B
102C
102D
102E
102F
102G
102H
103A
103B
103C
103D
103E
103F
103G
103H
104A
104B
104C
104D
104E
104F
104G
104H
105A
105C
105D
105E
105F
105G
105H
106A
106B
106C
106D
106E
106F
106G
106H
107A
107B
107C
107D
107E
107F
107H
108A
108B
108C
108E
108F
108G
108H
109A
109B
109C
109D
109E
109F
109G
109H
110A
110B
110C
110D
110E
110F
110G
110H
111A
111B
111D
111E
111F
111G
112A
112B
112D
112E
112F
112G
112H
113A
113B
113C
113D
113E
113H
114A
114B
114C
114E
114F
114G
114H
115A
115B
115C
115D
115E
115F
115G
115H
116A
116B
116C
116D
116F
116G
116H
117A
117B
117C
117D
117E
117F
117G
117H
118A
118B
118C
118D
118F
118G
118H
119A
119B
119C
119D
119E
119F
119G
119H
120A
120C
120D
120E
120F
120G
120H
121B
121C
121D
121E
121F
121G
122B
122C
122D
122E
122F
122G
122H
123A
123B
123C
123D
123E
123G
123H
124A
124B
124C
124D
124E
124F
124G
124H
BS00023201_51
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wsnp_Ex_rep_c106111_90308719
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Excalibur_c5139_198
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BobWhite_c39996_85
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Tdurum_contig43943_1165
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Tdurum_contig43943_56
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TA005766-0499
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If you need any more clarifications please let me know
system
March 3, 2022, 6:11pm
4
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