-
Notifications
You must be signed in to change notification settings - Fork 2
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
pep2qvalue missing? #26
Comments
Is this now computeFDR? |
Now works for me. Minor thing: Calculate Protein-level Q-valuescp <- pep2qvalue(scp, |
Excellent advice, thanks for pointing this out! I saw there were other places where I used |
pep2qvalue function appears missing. At least from the dev version.
BiocManager::install("UCLouvain-CBIO/scp") # Dev version
library("scp")
─ Packages ─────────────────────────────────────────────────────────────────────────────────────
! package * version date lib source
AnnotationFilter 1.14.0 2020-10-27 [1] Bioconductor
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
Biobase * 2.50.0 2020-10-27 [1] Bioconductor
BiocGenerics * 0.36.1 2021-04-16 [1] Bioconductor
V BiocManager 1.30.10 2021-06-15 [1] CRAN (R 4.0.2)
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.0.2)
cachem 1.0.5 2021-05-15 [1] CRAN (R 4.0.2)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.0.2)
cli 3.0.0 2021-06-30 [1] CRAN (R 4.0.2)
colorspace 2.0-2 2021-06-24 [1] CRAN (R 4.0.2)
crayon 1.4.1 2021-02-08 [1] CRAN (R 4.0.2)
curl 4.3.2 2021-06-23 [1] CRAN (R 4.0.2)
DBI 1.1.1 2021-01-15 [1] CRAN (R 4.0.2)
DelayedArray 0.16.3 2021-03-24 [1] Bioconductor
desc 1.3.0 2021-03-05 [1] CRAN (R 4.0.2)
devtools * 2.4.2 2021-06-07 [1] CRAN (R 4.0.2)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.2)
V dplyr 1.0.5 2021-06-18 [1] CRAN (R 4.0.2)
V ellipsis 0.3.1 2021-04-29 [1] CRAN (R 4.0.2)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.1)
V fansi 0.4.2 2021-05-25 [1] CRAN (R 4.0.2)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.0.2)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
generics 0.1.0 2020-10-31 [1] CRAN (R 4.0.2)
GenomeInfoDb * 1.26.7 2021-04-08 [1] Bioconductor
GenomeInfoDbData 1.2.4 2021-03-13 [1] Bioconductor
GenomicRanges * 1.42.0 2020-10-27 [1] Bioconductor
ggplot2 * 3.3.5 2021-06-25 [1] CRAN (R 4.0.2)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2)
htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.0.2)
IRanges * 2.24.1 2020-12-12 [1] Bioconductor
V knitr 1.31 2021-04-24 [1] CRAN (R 4.0.2)
lattice 0.20-44 2021-05-02 [1] CRAN (R 4.0.2)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.2)
lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.2)
magrittr * 2.0.1 2020-11-17 [1] CRAN (R 4.0.2)
MASS 7.3-54 2021-05-03 [1] CRAN (R 4.0.2)
Matrix 1.3-4 2021-06-01 [1] CRAN (R 4.0.2)
MatrixGenerics * 1.2.1 2021-01-30 [1] Bioconductor
matrixStats * 0.59.0 2021-06-01 [1] CRAN (R 4.0.2)
memoise 2.0.0 2021-01-26 [1] CRAN (R 4.0.2)
MsCoreUtils 1.2.0 2020-10-27 [1] Bioconductor
MultiAssayExperiment * 1.16.0 2020-10-27 [1] Bioconductor
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2)
V pillar 1.5.1 2021-05-16 [1] CRAN (R 4.0.2)
pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.0.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
pkgload 1.2.1 2021-04-06 [1] CRAN (R 4.0.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
processx 3.5.2 2021-04-30 [1] CRAN (R 4.0.2)
ProtGenerics 1.22.0 2020-10-27 [1] Bioconductor
ps 1.6.0 2021-02-28 [1] CRAN (R 4.0.2)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.2)
V QFeatures * 1.0.0 2021-07-17 [1] Github (rformassspectrometry/QFeatures@be2640e)
R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.2)
RCurl 1.98-1.3 2021-03-16 [1] CRAN (R 4.0.2)
remotes 2.4.0 2021-06-02 [1] CRAN (R 4.0.2)
V rlang 0.4.10 2021-04-30 [1] CRAN (R 4.0.2)
V rmarkdown 2.7 2021-06-15 [1] CRAN (R 4.0.2)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.2)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.0.2)
S4Vectors * 0.28.1 2020-12-09 [1] Bioconductor
scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2)
V scp * 1.0.0 2021-07-17 [1] Github (3127425)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
SingleCellExperiment 1.12.0 2020-10-27 [1] Bioconductor
SummarizedExperiment * 1.20.0 2020-10-27 [1] Bioconductor
testthat 3.0.4 2021-07-01 [1] CRAN (R 4.0.2)
V tibble 3.1.0 2021-05-16 [1] CRAN (R 4.0.2)
V tidyselect 1.1.0 2021-04-30 [1] CRAN (R 4.0.2)
V tinytex 0.30 2021-05-29 [1] CRAN (R 4.0.2)
usethis * 2.0.1 2021-02-10 [1] CRAN (R 4.0.2)
V utf8 1.1.4 2021-03-12 [1] CRAN (R 4.0.2)
V vctrs 0.3.6 2021-04-29 [1] CRAN (R 4.0.2)
withr 2.4.2 2021-04-18 [1] CRAN (R 4.0.2)
V xfun 0.22 2021-06-15 [1] CRAN (R 4.0.2)
XVector 0.30.0 2020-10-28 [1] Bioconductor
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2)
zlibbioc 1.36.0 2020-10-28 [1] Bioconductor
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library
V ── Loaded and on-disk version mismatch.
The text was updated successfully, but these errors were encountered: