Problem with check.marker after using recodeChromosome

Questions about GenABEL (aka *ABEL) suite of packages
Forum rules
Please remember not to post any sensitive data on this public forum.
The first few posts of newly registered users will be moderated in order to filter out any spammers.

When get a solution to the problem you posted, please change the topic name (e.g. from "how to ..." to "[SOLVED] how to ..."). This will make it easier for the community to follow the posts yet to be attended.
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?


Relevant commands and output below.

Code: Select all

qc <-check.marker(BirdData,call=0.70,,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

Return to “GenABEL”

Who is online

Users browsing this forum: No registered users and 2 guests