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meyer-lab-cshl / plinkQC

R package for quality control of plink genetic datasets
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Error using the evaluate_check_ancestry function #48

Open boseb opened 2 years ago

boseb commented 2 years ago

Hi, I am using "evaluate_check_ancestry" functions with the data files provided in extdata by plinkQC and my data as well. In both cases, I am getting the error: Error in seq_len(n) : argument must be coercible to non-negative integer In addition: Warning messages: 1: In max(all_european$euclid_dist) : no non-missing arguments to max; returning -Inf 2: Removed 1 rows containing non-finite values (stat_circle). 3: In max(f) : no non-missing arguments to max; returning -Inf

To Reproduce My script: indir <- "/projects/b1137/BBose/ProjectGWAS/reference/PlinkQC_data/extdata" qcdir <-indir ancestry_check <- evaluate_check_ancestry(indir=indir, name="data.HapMapIII", prefixMergedDataset="data.HapMapIII", refSamplesFile=paste(indir, "/HapMap_ID2Pop.txt", sep=""), refColorsFile=paste(indir, "/HapMap_PopColors.txt", sep=""), refPopulation = "CEU", interactive=TRUE)

I used library(devtools) install_github("meyer-lab-cshl/plinkQC", ref="dev" )

─ Session info ──────────────────────────────────────────────────────────────────────────────────── setting value
version R version 4.1.1 (2021-08-10)
os Red Hat Enterprise Linux Server 7.5 (Maipo) system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Chicago
date 2022-03-25

─ Packages ──────────────────────────────────────────────────────────────────────────────────────── package version date lib source
annotate 1.68.0 2020-10-27 [1] Bioconductor
AnnotationDbi 1.52.0 2020-10-27 [1] Bioconductor
askpass 1.1 2019-01-13 [1] CRAN (R 4.0.3)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.3)
bcellViper 1.26.0 2020-10-29 [1] Bioconductor
Biobase 2.50.0 2020-10-27 [1] Bioconductor
BiocFileCache 1.14.0 2020-10-27 [1] Bioconductor
BiocGenerics 0.36.1 2021-04-16 [1] Bioconductor
biomaRt 2.46.3 2021-02-09 [1] Bioconductor
bit 4.0.4 2020-08-04 [1] CRAN (R 4.0.3)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.0.3)
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.0.3)
blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.3)
cachem 1.0.5 2021-05-15 [1] CRAN (R 4.0.3)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.0.3)
cli 2.5.0 2021-04-26 [1] CRAN (R 4.0.3)
CNTools 1.46.0 2020-10-27 [1] Bioconductor
colorspace 2.0-1 2021-05-04 [1] CRAN (R 4.0.3)
cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.0.3)
crayon 1.4.1 2021-02-08 [1] CRAN (R 4.0.3)
curl 4.3.1 2021-04-30 [1] CRAN (R 4.0.3)
data.table 1.14.0 2021-02-21 [1] CRAN (R 4.0.3)
DBI 1.1.1 2021-01-15 [1] CRAN (R 4.0.3)
dbplyr 2.1.1 2021-04-06 [1] CRAN (R 4.0.3)
DelayedArray 0.16.3 2021-03-24 [1] Bioconductor
desc 1.3.0 2021-03-05 [1] CRAN (R 4.0.3)
devtools 2.4.2 2021-06-07 [1] CRAN (R 4.0.3)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.3)
dorothea 1.5.0 2021-09-09 [1] Github (saezlab/dorothea@acb11b1)
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dplyr 1.0.6 2021-05-05 [1] CRAN (R 4.0.3)
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fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.0.3)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.3)
gaston 1.5.7 2020-09-24 [1] CRAN (R 4.0.3)
gdsfmt 1.26.1 2020-12-22 [1] Bioconductor
genefilter 1.72.1 2021-01-21 [1] Bioconductor
generics 0.1.0 2020-10-31 [1] CRAN (R 4.0.3)
GenomeInfoDb 1.26.7 2021-04-08 [1] Bioconductor
GenomeInfoDbData 1.2.4 2021-06-08 [1] Bioconductor
GenomicRanges 1.42.0 2020-10-27 [1] Bioconductor
getopt 1.20.3 2019-03-22 [1] CRAN (R 4.1.1)
ggforce 0.3.3 2021-03-05 [1] CRAN (R 4.0.3)
ggfortify 0.4.14 2022-01-03 [1] CRAN (R 4.1.1)
ggplot2 3.3.5 2021-06-25 [1] CRAN (R 4.0.3)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.3)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.3)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.3)
hms 1.1.0 2021-05-17 [1] CRAN (R 4.0.3)
httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.3)
IRanges 2.24.1 2020-12-12 [1] Bioconductor
jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.0.3)
knitr 1.33 2021-04-24 [1] CRAN (R 4.0.3)
lattice 0.20-44 2021-05-02 [2] CRAN (R 4.1.1)
lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.3)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.3)
MASS 7.3-54 2021-05-03 [2] CRAN (R 4.1.1)
Matrix 1.3-4 2021-06-01 [1] CRAN (R 4.0.3)
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openssl 1.4.4 2021-04-30 [1] CRAN (R 4.0.3)
optparse 1.7.1 2021-10-08 [1] CRAN (R 4.1.1)
pillar 1.6.1 2021-05-16 [1] CRAN (R 4.0.3)
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pkgload 1.2.1 2021-04-06 [1] CRAN (R 4.0.3)
plinkQC 0.3.4 2022-03-25 [1] Github (meyer-lab-cshl/plinkQC@1dc9057)
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R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.3)
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RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.3)
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stringi 1.6.2 2021-05-17 [1] CRAN (R 4.0.3)
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survival 3.2-11 2021-04-26 [2] CRAN (R 4.1.1)
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tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.0.3)
tweenr 1.0.2 2021-03-23 [1] CRAN (R 4.0.3)
UpSetR 1.4.0 2019-05-22 [1] CRAN (R 4.1.1)
usethis 2.0.1 2021-02-10 [1] CRAN (R 4.0.3)
utf8 1.2.1 2021-03-12 [1] CRAN (R 4.0.3)
vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.0.3)
withr 2.4.2 2021-04-18 [1] CRAN (R 4.0.3)
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XML 3.99-0.6 2021-03-16 [1] CRAN (R 4.0.3)
xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.3)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.3)
XVector 0.30.0 2020-10-27 [1] Bioconductor
zlibbioc 1.36.0 2020-10-27 [1] Bioconductor

I have seen this bug is reported previously, however it is not fixed yet. Please help. Thanks, Bose

HannahVMeyer commented 2 years ago

I am currently on maternity leave, but will try to have a look in the next few weeks. Thanks