check.marker and maf

Questions about GenABEL (aka *ABEL) suite of packages
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kapr_genabel
Posts: 3
Joined: Wed Mar 23, 2016 10:30 am

check.marker and maf

Postby kapr_genabel » Tue Jul 12, 2016 2:02 pm

Hello @all

I working on genome wide association analysis with GenABEL, of fungal genome data, with more than a million SNPs.

I am able to do descriptives.trait and descriptives.marker scan of my genotype and phenotype and descriptive.scan of raw data.

But when i go quality check of my data with check.marker i get bellow error. but i don't understand what the error is about.

also, would like to do descriptives.marker MAF of (0.35 and 0.25), i have tried but i get the same result as show in the qqplot. could some some help in sharing the script to do descriptives.scan of the marker data that has 0,35 and 0.25 MAF.

Thank you
KRP

Code: Select all

[*]gwadata <- load.gwaa.data(phenofile="phenomean.dat",genofile="quali-fil-scaf58.raw")
ids loaded...
marker names loaded...
chromosome data loaded...
map data loaded...
allele coding data loaded...
strand data loaded...
genotype data loaded...
snp.data object created...
assignment of gwaa.data object FORCED; X-errors were not checked!
qc1 <- check.marker(gwadata)
Excluding people/markers with extremely low call rate...
1019387 markers and 29 people in total
0 people excluded because of call rate < 0.1
958 markers excluded because of call rate < 0.1
Passed: 1018429 markers and 29 people

RUN 1
1018429 markers and 29 people in total
231574 (22.73835%) markers excluded as having low (<8.62069%) minor allele frequency
332801 (32.67788%) markers excluded because of low (<95%) call rate
1018429 (100%) markers excluded because they are out of HWE (FDR <0.2)

Error in .local(x, i, j, ..., drop) : j out of range (== 0) In
 addition: Warning message: In max(j) : no non-missing arguments to
 max; returning -Inf
 
Last edited by lckarssen on Wed Jul 13, 2016 11:01 am, edited 1 time in total.
Reason: Formatted R code using [code] tags

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