Changing the number of significant digits in a DETable undoes any sorting that has been done before.
Example:
library(iSEEde)
library(airway)
library(DESeq2)
library(iSEE)
data("airway")
airway$dex <- relevel(airway$dex, "untrt")
dds <- DESeqDataSet(airway, ~ 0 + dex + cell)
dds <- DESeq(dds)
res_deseq2 <- results(dds, contrast = list("dextrt", "dexuntrt"))
airway <- embedContrastResults(res_deseq2, airway, name = "dex: trt vs untrt")
iSEE(airway, initial = list(
DETable(ContrastName="dex: trt vs untrt")
))
- Sort by baseMean
- Check 'Round digits'
-> table is unsorted
R session information
Session info
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.3.1 (2023-06-16)
os macOS Ventura 13.5.1
system aarch64, darwin20
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Zurich
date 2023-09-06
rstudio 2023.06.1+524 Mountain Hydrangea (desktop)
pandoc 3.1.7 @ /opt/homebrew/bin/pandoc
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0)
airway * 1.21.0 2023-04-27 [1] Bioconductor
Biobase * 2.61.0 2023-06-02 [1] Bioconductor
BiocGenerics * 0.47.0 2023-06-02 [1] Bioconductor
BiocParallel 1.35.4 2023-08-17 [1] Bioconductor
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.3.0)
bslib 0.5.1 2023-08-11 [1] CRAN (R 4.3.0)
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.0)
circlize 0.4.15 2022-05-10 [1] CRAN (R 4.3.0)
cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0)
clue 0.3-64 2023-01-31 [1] CRAN (R 4.3.0)
cluster 2.1.4 2022-08-22 [2] CRAN (R 4.3.1)
codetools 0.2-19 2023-02-01 [2] CRAN (R 4.3.1)
colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0)
colourpicker 1.3.0 2023-08-21 [1] CRAN (R 4.3.0)
ComplexHeatmap 2.17.0 2023-06-02 [1] Bioconductor
crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0)
DelayedArray 0.27.10 2023-07-28 [1] Bioconductor
DESeq2 * 1.41.8 2023-08-20 [1] Bioconductor
digest 0.6.33 2023-07-07 [1] CRAN (R 4.3.0)
doParallel 1.0.17 2022-02-07 [1] CRAN (R 4.3.0)
dplyr 1.1.3 2023-09-03 [1] CRAN (R 4.3.0)
DT 0.29 2023-08-29 [1] CRAN (R 4.3.0)
edgeR 3.43.8 2023-08-02 [1] Bioconductor
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.0)
fansi 1.0.4 2023-01-22 [1] CRAN (R 4.3.0)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
foreach 1.5.2 2022-02-02 [1] CRAN (R 4.3.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
GenomeInfoDb * 1.37.3 2023-08-28 [1] Bioconductor
GenomeInfoDbData 1.2.10 2023-05-03 [1] Bioconductor
GenomicRanges * 1.53.1 2023-06-02 [1] Bioconductor
GetoptLong 1.0.5 2020-12-15 [1] CRAN (R 4.3.0)
ggplot2 3.4.3 2023-08-14 [1] CRAN (R 4.3.0)
ggrepel 0.9.3 2023-02-03 [1] CRAN (R 4.3.0)
GlobalOptions 0.1.2 2020-06-10 [1] CRAN (R 4.3.0)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0)
gtable 0.3.4 2023-08-21 [1] CRAN (R 4.3.0)
htmltools 0.5.6 2023-08-10 [1] CRAN (R 4.3.0)
htmlwidgets 1.6.2 2023-03-17 [1] CRAN (R 4.3.0)
httpuv 1.6.11 2023-05-11 [1] CRAN (R 4.3.0)
igraph 1.5.1 2023-08-10 [1] CRAN (R 4.3.0)
IRanges * 2.35.2 2023-06-23 [1] Bioconductor
iSEE * 2.13.5 2023-07-26 [1] Bioconductor
iSEEde * 0.99.0 2023-05-18 [1] Github (iSEE/iSEEde@dc2eb18)
iterators 1.0.14 2022-02-05 [1] CRAN (R 4.3.0)
jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.3.0)
jsonlite 1.8.7 2023-06-29 [1] CRAN (R 4.3.0)
later 1.3.1 2023-05-02 [1] CRAN (R 4.3.0)
lattice 0.21-8 2023-04-05 [2] CRAN (R 4.3.1)
lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.3.0)
limma 3.57.7 2023-08-02 [1] Bioconductor
locfit 1.5-9.8 2023-06-11 [1] CRAN (R 4.3.0)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
Matrix 1.6-1 2023-08-14 [2] CRAN (R 4.3.0)
MatrixGenerics * 1.13.1 2023-07-26 [1] Bioconductor
matrixStats * 1.0.0 2023-06-02 [1] CRAN (R 4.3.0)
mgcv 1.9-0 2023-07-11 [2] CRAN (R 4.3.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.3.0)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.0)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0)
nlme 3.1-163 2023-08-09 [2] CRAN (R 4.3.0)
pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0)
promises 1.2.1 2023-08-10 [1] CRAN (R 4.3.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.3.0)
Rcpp 1.0.11 2023-07-06 [1] CRAN (R 4.3.0)
RCurl 1.98-1.12 2023-03-27 [1] CRAN (R 4.3.0)
rintrojs 0.3.2 2022-08-09 [1] CRAN (R 4.3.0)
rjson 0.2.21 2022-01-09 [1] CRAN (R 4.3.0)
rlang 1.1.1 2023-04-28 [1] CRAN (R 4.3.0)
rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.0)
S4Arrays 1.1.6 2023-08-31 [1] Bioconductor
S4Vectors * 0.39.1 2023-06-02 [1] Bioconductor
sass 0.4.7 2023-07-15 [1] CRAN (R 4.3.0)
scales 1.2.1 2022-08-20 [1] CRAN (R 4.3.0)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
shape 1.4.6 2021-05-19 [1] CRAN (R 4.3.0)
shiny 1.7.5 2023-08-12 [1] CRAN (R 4.3.0)
shinyAce 0.4.2 2022-05-06 [1] CRAN (R 4.3.0)
shinydashboard 0.7.2 2021-09-30 [1] CRAN (R 4.3.0)
shinyjs 2.1.0 2021-12-23 [1] CRAN (R 4.3.0)
shinyWidgets 0.8.0 2023-08-30 [1] CRAN (R 4.3.0)
SingleCellExperiment * 1.23.0 2023-04-25 [1] Bioconductor
SparseArray 1.1.12 2023-08-31 [1] Bioconductor
statmod 1.5.0 2023-01-06 [1] CRAN (R 4.3.0)
SummarizedExperiment * 1.31.1 2023-05-01 [1] Bioconductor
tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0)
tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0)
utf8 1.2.3 2023-01-31 [1] CRAN (R 4.3.0)
vctrs 0.6.3 2023-06-14 [1] CRAN (R 4.3.0)
vipor 0.4.5 2017-03-22 [1] CRAN (R 4.3.0)
viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.0)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.0)
XVector 0.41.1 2023-06-02 [1] Bioconductor
zlibbioc 1.47.0 2023-05-20 [1] Bioconductor
[1] /Users/charlottesoneson/Documents/Software/Rlib/Bioc3.18
[2] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Changing the number of significant digits in a
DETableundoes any sorting that has been done before.Example:
-> table is unsorted
R session information
Session info