Problem in G G` statistic calculation: Error in locfit::locfit(Stat ~ locfit::lp(POS, h = windowSize, deg = 0), : fewer than one row in the data about qtlseqr

[bmansfeld]

Hi,
I think the problem is due to the assembly and the window size.
But just to make sure, what happens if you run runQTLseqAnalysis() first?
Does it work? after it works can you run Gprime on the new df that comes out of runQTLseqAnalysis?

If not try lowering the window size and perhaps try discarding many of the very small contigs.
Let me know what you find out..
I'll try to help as best as possible
Ben

[anjugiri]

Hi Ben,

Thank you for your response.

Lowering the window size doesn't help, I will try by dropping some contigs.
QTLseqAnalysis runs without error, and attached above (df_filt) is the df frame generated after running QTLseqAnalysis as follows:

df_filt <- runQTLseqAnalysis(df_filt, windowSize = 1e6,

•                                popStruc = "F2",
  

•                                bulkSize = c(78,103), replications = 10000,
  

•                                intervals = c(95, 99) )
  

The Gprime is on the df df_filt that comes out of the runQTLseqAnalysis, but doesn't seem to help.

I will let try more with additional filtering in the contigs and will let you know.

Thank you,
Anju

[bmansfeld]

Hey Anju,
Did you figure this out?
If not and you feel comfortable sharing your .table file I can take a look.
Let me know,
Ben

[anjugiri]

C32_w_parents_allsites.vcf.table.zip

Ben, Thank you very much. Here is the data frame I worked with, I tried with several different files but got into the same error. To start, I just filtered to remove NAs from the file.

[anjugiri]

Never mind. The issue get solved after filtering. Thank you very much, the package is very helpful.

[bmansfeld]

Thanks for letting me know and for the good feedback!
Would you mind explaining what you think the issue was.
This way if other people have a similar problem they can see what solved it.
Thanks,
Ben

[anjugiri]

Some of the contigs were very short (in Kbs) and the window in them had very few SNP, I did filter for windows having at least 5 SNP which helped to solve this issue. Thank you for your suggestion.