OmicsQC
Nominating Quality Control Outliers in Genomic Profiling Studies
v1.1.1
·
Jan 23, 2026
·
GPL-2
Description
A method that analyzes quality control metrics from multi-sample genomic sequencing studies and nominates poor quality samples for exclusion. Per sample quality control data are transformed into z-scores and aggregated. The distribution of aggregated z-scores are modelled using parametric distributions. The parameters of the optimal model, selected either by goodness-of-fit statistics or user-designation, are used for outlier nomination. Two implementations of the Cosine Similarity Outlier Detection algorithm are provided with flexible parameters for dataset customization.
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Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | ERROR |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (14 non-OK)
OK
r-devel-linux-x86_64-debian-clang
*
ERROR
r-devel-linux-x86_64-debian-gcc
tests
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat);
>
> test_check('OmicsQC')
Loading required package: OmicsQC
Saving _problems/test-plotting-127.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 66 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plotting.R:124:3'): get.qc.multipanelplot ────────────────────
Expected `get.qc.multipanelplot(barplot = bp, heatmap = hm)` not to throw any errors.
Actually got a <simpleError> with message:
a character vector argument expected
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-plotting.R:124:3
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─OmicsQC::get.qc.multipanelplot(barplot = bp, heatmap = hm)
8. └─BoutrosLab.plotting.general::create.multipanelplot(...)
9. └─BoutrosLab.plotting.general:::get.legend.height(...)
10. └─tools::file_ext(filename)
11. ├─base::ifelse(...)
12. ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
13. │ └─base::is.factor(x)
14. └─base::basename(x)
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 66 ]
Error:
! Test failures.
Execution halted
OK
r-devel-linux-x86_64-fedora-clang
*
OK
r-devel-linux-x86_64-fedora-gcc
*
OK
r-devel-macos-arm64
*
OK
r-devel-windows-x86_64
*
OK
r-oldrel-macos-arm64
*
OK
r-oldrel-macos-x86_64
*
OK
r-oldrel-windows-x86_64
*
OK
r-patched-linux-x86_64
*
OK
r-release-linux-x86_64
*
OK
r-release-macos-arm64
*
OK
r-release-macos-x86_64
*
OK
r-release-windows-x86_64
*
Check History
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 9, 2026
ERROR
r-devel-linux-x86_64-debian-gcc
tests
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat);
>
> test_check('OmicsQC')
Loading required package: OmicsQC
Saving _problems/test-plotting-127.R
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 66 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-plotting.R:124:3'): get.qc.multipanelplot ────────────────────
Expected `get.qc.multipanelplot(barplot = bp, heatmap = hm)` no
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new
1.1.1
Mar 9, 2026