Problem with check.marker after using recodeChromosome

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jslate
Posts: 1
Joined: Wed Jun 03, 2015 1:23 pm

Problem with check.marker after using recodeChromosome

Postby jslate » Wed Jun 03, 2015 2:17 pm

Hello all

I am working on a bird species with more than 30 chromosomes.
I can happily input .tped and .tped files from Plink and run an analysis in GenABEL.
However, in Plink, my sex chromosome is coded 35, and I want GenABEL to know it is not autosomal.

I can recode this as X using the recodeChromosome function.
BirdData<- recodeChromosome(BirdData,rules=list("35"="X"))
Recoded chromosome for 28650 SNPs ( 35 -> X )

[Note that birds are actually ZZ male / ZW female, so the 'X' here corresponds to the 'Z' and I have swapped the male and females around in the sex column, such that males are 0 and females are 1, to account for females being heterogametic]

However, after doing this, I had a problem with check.marker, such that it now hangs at the 'Passed: X markers and Y people' stage, before doing the quality control.
This doesn't happen when I run the same file but with the sex chromosome still coded as an integer.

I wonder whether the problem is because I still have heterozygous male (really female) genotypes.
However, it seems that Xfix() should only be run to correct these AFTER running check.marker.
Anyone else encoutnered this problem/got a solution?

Jon



Relevant commands and output below.

Code: Select all

qc <-check.marker(BirdData,call=0.70,perid.call=0.50,p.level=1e-5,maf=0.05)

Excluding people/markers with extremely low call rate...
494705 markers and 491 people in total
0 people excluded because of call rate < 0.1
0 markers excluded because of call rate < 0.1
Passed: 494705 markers and 491 people

Running sex chromosome checks...
53272 heterozygous X-linked male genotypes found
402 X-linked markers are likely to be autosomal (odds > 1000 )
0 male are likely to be female (odds > 1000 )
0 female are likely to be male (odds > 1000 )
0 people have intermediate X-chromosome inbreeding (0.5 > F > 0.5)
If these people/markers are removed, 32844 heterozygous male genotypes are left
... these will be considered missing in analysis.
... Use Xfix() to fix these problems.
Passed: 494303 markers and 491 people
Last edited by lckarssen on Fri Jun 05, 2015 10:59 am, edited 1 time in total.
Reason: Reformatted part of the input and output with the [code] tag

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