Error in data.frame

[Lsteenhuis]

Dear Qing,

I have been trying to get giremi running over the past few weeks, and used the issues on this page to try to solve my problems.
But now I have the following error:

dat.pos <- cbind(dat.pos[,c("upstream_1base","downstream_1base")],abs(dat.pos[,"major_ratio"]-dat.pos[,"estimated_allelic_ratio"]),1)
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 0, 1
Calls: cbind -> cbind -> data.frame
Execution halted

I have seen you suggest to remove the homozygous SNV's from the list, I think I have done this correctly but the error persists.
The output files and my list of SNV's are attached and I would greatly appreciate it if you could take some of your time to help me figure out this problem.

giremi_out.txt
giremi_out.vcf.Rout.txt
test_snps.txt

Cheers,

Lars

[zhqingit]

Hi Lars,

When you run giremi, you can see the meanMI and sdMI in the screen, could
you send me the two values? Thanks.

Best,
Qing

2016-10-10 1:41 GMT-07:00 Lsteenhuis notifications@github.com:

Dear Qing,

I have been trying to get giremi running over the past few weeks, and used
the issues on this page to try to solve my problems.
But now I have the following error:

dat.pos <- cbind(dat.pos[,c("upstream_1base","downstream_1base")],
abs(dat.pos[,"major_ratio"]-dat.pos[,"estimated_allelic_ratio"]),1)
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 0, 1
Calls: cbind -> cbind -> data.frame
Execution halted

I have seen you suggest to remove the homozygous SNV's from the list, I
think I have done this correctly but the error persists.
The output files and my list of SNV's are attached and I would greatly
appreciate it if you could take some of your time to help me figure out
this problem.

giremi_out.txt
https://github.com/zhqingit/giremi/files/519046/giremi_out.txt
giremi_out.vcf.Rout.txt
https://github.com/zhqingit/giremi/files/519049/giremi_out.vcf.Rout.txt
test_snps.txt
https://github.com/zhqingit/giremi/files/519052/test_snps.txt

Cheers,

Lars

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[Lsteenhuis]

Hey Qing,

Thanks for the quick reaction, my meanMI and sdMI are:

meanMI:0.004893 sdMI:0.028364

It caught my eye that these values are really low.
I have seen you suggest to use more stringent SNV calling, do you also suggest to increase the stringency of the filters?

Thanks in advance,

Lars

[zhqingit]

Hi Lars,

Yes, I think your SNP list is not pure, there must be many sequencing
errors. So please try more strict filters.

Best,
Qing

2016-10-11 7:38 GMT-07:00 Lsteenhuis notifications@github.com:

Hey Qing,

Thanks for the quick reaction, my meanMI and sdMI are:

meanMI:0.004893 sdMI:0.028364

It caught my eye that these values are really low.
I have seen you suggest to use more stringent SNV calling, do you also
suggest to increase the stringency of the filters?

Thanks in advance,

Lars

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[Lsteenhuis]

Hey Qing,

Alright I will play around some more, thanks for the help!
I will close the threat since I know what to do now.

Cheers,

Lars