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kbroman / qtl

R/qtl: A QTL mapping environment
https://rqtl.org
GNU General Public License v3.0
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Error: "long vectors (argument 5) are not supported in .C" #97

Closed jeancarlier34 closed 2 years ago

jeancarlier34 commented 2 years ago

Hello,

I'm running r/qtl to construct a map. Here the input file:

--Read the following data: 132 individuals 4574 markers 1 phenotypes --Cross type: haploid Haploids

No. individuals:    132 

No. phenotypes:     1 
Percent phenotyped: 100 

No. chromosomes:    20 
    Autosomes:      1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 

Total markers:      4574 
No. markers:        724 679 501 390 359 328 324 297 297 246 192 48 39 35 35 
                    26 24 24 4 2 
Percent genotyped:  82.4 
Genotypes (%):      A:49.7  B:50.3

I run this function on all chromosome:

data=orderMarkers(data, chr=20, use.ripple=TRUE, error.prob=0.001, map.function=c("kosambi")) pull.map(data, chr=20)

It work for all except the first one which is also the longest with 724 markers. I got the following error: "long vectors (argument 5) are not supported in .C"

It's not a memory issu.

Do you know how to solve it? Thanks, Jean Carlier

kbroman commented 2 years ago

Try reducing the value for window, say window=3, or use.ripple = FALSE

kbroman commented 2 years ago

This is effectively a memory issue, as the object with the possible orders of 724 markers, considering all permutations in a sliding window of 7 markers, makes the results object too large to store.