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UCLouvain-CBIO / scp

Single cell proteomics data processing
https://uclouvain-cbio.github.io/scp/index.html
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pep2qvalue missing? #26

Closed edemmott closed 3 years ago

edemmott commented 3 years ago

pep2qvalue function appears missing. At least from the dev version.

BiocManager::install("UCLouvain-CBIO/scp") # Dev version

library("scp")

session_info() ─ Session info ───────────────────────────────────────────────────────────────────────────────── setting value
version R version 4.0.4 (2021-02-15) os macOS Catalina 10.15.6
system x86_64, darwin17.0
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/London
date 2021-07-18

─ 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 (UCLouvain-CBIO/scp@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.

edemmott commented 3 years ago

Is this now computeFDR?

edemmott commented 3 years ago

Now works for me. Minor thing: groupBy term needed changing from the vignette. Maxquant standard output could be done using 'Leading.razor.protein' as below or 'Proteins'/'Leading.proteins'. In the vignette this is simply 'protein' which doesn't work with unmodified maxquant files. Code below seems to work fine.

Calculate Protein-level Q-value

scp <- pep2qvalue(scp, i = 1:96, PEP = "dart_PEP", groupBy = "Leading.razor.protein", rowDataName = "qvalue_proteins")

cvanderaa commented 3 years ago

Excellent advice, thanks for pointing this out! I saw there were other places where I used protein that I now replaced by Leading.razor.protein for consistency. The vignette is updated and so will the online documentation soon.