HannahVMeyer
commented
3 years ago apologies, I missed this issue. In the command above, you specify interactive=FALSE, so it will not create the plot automatically. You can set interactive=TRUE to plot the result while running the function. In either case, you can access the plot from the results object fail_sex$p_sexcheck, documented in the Value section of the function accessible via ?check_sex.
Describe the bug A clear and concise description of what the bug is. The plot mentioned bellow: Step-by-step: Individuals with discordant sex information in https://cran.r-project.org/web/packages/plinkQC/vignettes/plinkQC.pdf was not created! I am running the mentioned command and I am getting Rplots.pdf but when I try to open it it says hat the file is damaged. I am using R 3.6.3
I am creating a basic plot in R and saving it as .pdf and it works:
To Reproduce Provide a minimal example of what you re trying to do. If you rely on some external data, please provide a link to a small, sample dataset.
library(plinkQC) indir <- getwd() qcdir <-getwd() name='data' path2plink <- "/projects/plink" package.dir <-find.package('plinkQC')
fail_sex <-check_sex(indir=indir, qcdir=qcdir, name=name, interactive=FALSE,verbose=TRUE, path2plink=path2plink)
Expected behavior A clear and concise description of what you expected to happen.
Error messages Show the error messages received when executing the steps outlined above.
128528 MB RAM detected; reserving 64264 MB for main workspace. 437855 variants loaded from .bim file. 1777 people (814 males, 963 females) loaded from .fam. Using 1 thread (no multithreaded calculations invoked). Before main variant filters, 1777 founders and 0 nonfounders present. Calculating allele frequencies... done. Warning: 36546 het. haploid genotypes present (see /projects/com_grassim/anamaria/anamaria/anamaria/GOKIND/75327/PhenoGenotypeFiles/RootStudyConsentSet_phs000018.GAIN_GoKinD.v2.p1.c1.DS-T1DCR-IRB/GenotypeFiles/Output/test/qcdir/data.hh ); many commands treat these as missing. Total genotyping rate is 0.973208. 437855 variants and 1777 people pass filters and QC. Note: No phenotypes present. --check-sex: 9750 Xchr and 0 Ychr variant(s) scanned, 5 problems detected. Report written to /projects/com_grassim/anamaria/anamaria/anamaria/GOKIND/75327/PhenoGenotypeFiles/RootStudyConsentSet_phs000018.GAIN_GoKinD.v2.p1.c1.DS-T1DCR-IRB/GenotypeFiles/Output/test/qcdir/data.sexcheck .
128528 MB RAM detected; reserving 64264 MB for main workspace. 437855 variants loaded from .bim file. 1777 people (814 males, 963 females) loaded from .fam. Using 1 thread (no multithreaded calculations invoked). Before main variant filters, 1777 founders and 0 nonfounders present. Calculating allele frequencies... done. Warning: 36546 het. haploid genotypes present (see /projects/com_grassim/anamaria/anamaria/anamaria/GOKIND/75327/PhenoGenotypeFiles/RootStudyConsentSet_phs000018.GAIN_GoKinD.v2.p1.c1.DS-T1DCR-IRB/GenotypeFiles/Output/test/qcdir/data.hh ); many commands treat these as missing. Total genotyping rate is 0.973208. 437855 variants and 1777 people pass filters and QC. Note: No phenotypes present. --check-sex: 9750 Xchr and 0 Ychr variant(s) scanned, 5 problems detected. Report written to /projects/com_grassim/anamaria/anamaria/anamaria/GOKIND/75327/PhenoGenotypeFiles/RootStudyConsentSet_phs000018.GAIN_GoKinD.v2.p1.c1.DS-T1DCR-IRB/GenotypeFiles/Output/test/qcdir/data.sexcheck .
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