missing function queryConsensusPeaks in Bioc v.2.10.0
Closed this issue · 2 comments
Hi,
I am trying to follow the bioconductor vignette for ENCODEExplorer and when I try to obtain consensus Peaks from ChIP-Seq (section 5.1) I get the following error:
res = queryConsensusPeaks("22Rv1", "GRCh38", "CTCF")
Error in queryConsensusPeaks("22Rv1", "GRCh38", "CTCF"):
could not find function "queryConsensusPeaks"It looks like the function is not part of the package anymore? I also looked into package ENCODExplorerData, but to no avail... Could you point me to the function? thanks!
session info:
-
Session info --------------------------------------------------
setting value
version R version 3.6.2 (2019-12-12)
os Windows 10 x64
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz America/New_York
date 2020-02-16 -
Packages ------------------------------------------------------
package * version date lib source
AnnotationDbi * 1.46.1 2019-08-20 [1] Bioconductor
AnnotationFilter * 1.8.0 2019-05-02 [1] Bioconductor
AnnotationHub * 2.16.1 2019-09-04 [1] Bioconductor
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.1)
backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.1)
Biobase * 2.44.0 2019-05-02 [1] Bioconductor
BiocFileCache * 1.8.0 2019-05-02 [1] Bioconductor
BiocGenerics * 0.30.0 2019-05-02 [1] Bioconductor
BiocManager 1.30.10 2019-11-16 [1] CRAN (R 3.6.1)
BiocParallel 1.18.1 2019-08-06 [1] Bioconductor
biomaRt 2.40.5 2019-10-01 [1] Bioconductor
Biostrings 2.52.0 2019-05-02 [1] Bioconductor
bit 1.1-15.1 2020-01-14 [1] CRAN (R 3.6.2)
bit64 0.9-7 2017-05-08 [1] CRAN (R 3.6.0)
bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0)
blob 1.2.1 2020-01-20 [1] CRAN (R 3.6.2)
boot 1.3-24 2019-12-20 [2] CRAN (R 3.6.2)
broom 0.5.4 2020-01-27 [1] CRAN (R 3.6.2)
callr 3.4.2 2020-02-12 [1] CRAN (R 3.6.2)
caTools 1.18.0 2020-01-17 [1] CRAN (R 3.6.2)
cellranger 1.1.0 2016-07-27 [1] CRAN (R 3.6.1)
checkmate 2.0.0 2020-02-06 [1] CRAN (R 3.6.2)
cli 2.0.1 2020-01-08 [1] CRAN (R 3.6.2)
codetools 0.2-16 2018-12-24 [2] CRAN (R 3.6.2)
colorRamps 2.3 2012-10-29 [1] CRAN (R 3.6.0)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.1)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
curl 4.3 2019-12-02 [1] CRAN (R 3.6.1)
data.table 1.12.8 2019-12-09 [1] CRAN (R 3.6.2)
DBI 1.1.0 2019-12-15 [1] CRAN (R 3.6.2)
dbplyr * 1.4.2 2019-06-17 [1] CRAN (R 3.6.1)
DelayedArray 0.10.0 2019-05-02 [1] Bioconductor
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.1)
devtools 2.2.1 2019-09-24 [1] CRAN (R 3.6.1)
digest 0.6.23 2019-11-23 [1] CRAN (R 3.6.1)
doParallel 1.0.15 2019-08-02 [1] CRAN (R 3.6.1)
dplyr * 0.8.4 2020-01-31 [1] CRAN (R 3.6.2)
DT * 0.12 2020-02-05 [1] CRAN (R 3.6.2)
edgeR * 3.26.8 2019-09-01 [1] Bioconductor
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.1)
ENCODExplorer * 2.10.0 2019-05-02 [1] Bioconductor
ENCODExplorerData * 0.99.1 2020-02-16 [1] Bioconductor
ensembldb * 2.8.1 2019-10-11 [1] Bioconductor
fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.2)
fastmap 1.0.1 2019-10-08 [1] CRAN (R 3.6.1)
forcats * 0.4.0 2019-02-17 [1] CRAN (R 3.6.1)
foreach * 1.4.8 2020-02-09 [1] CRAN (R 3.6.2)
fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.1)
gdata 2.18.0 2017-06-06 [1] CRAN (R 3.6.0)
generics 0.0.2 2018-11-29 [1] CRAN (R 3.6.1)
GenomeInfoDb * 1.20.0 2019-05-02 [1] Bioconductor
GenomeInfoDbData 1.2.1 2019-11-30 [1] Bioconductor
GenomicAlignments 1.20.1 2019-06-18 [1] Bioconductor
GenomicFeatures * 1.36.4 2019-07-11 [1] Bioconductor
GenomicRanges * 1.36.1 2019-09-06 [1] Bioconductor
ggplot2 * 3.2.1 2019-08-10 [1] CRAN (R 3.6.1)
glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.1)
gplots 3.0.1.2 2020-01-11 [1] CRAN (R 3.6.2)
graph 1.62.0 2019-05-02 [1] Bioconductor
graphite * 1.30.0 2019-05-02 [1] Bioconductor
gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.1)
gtools 3.8.1 2018-06-26 [1] CRAN (R 3.6.0)
haven 2.2.0 2019-11-08 [1] CRAN (R 3.6.1)
hms 0.5.3 2020-01-08 [1] CRAN (R 3.6.2)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.1)
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 3.6.1)
httpuv 1.5.2 2019-09-11 [1] CRAN (R 3.6.1)
httr 1.4.1 2019-08-05 [1] CRAN (R 3.6.1)
interactiveDisplayBase 1.22.0 2019-05-02 [1] Bioconductor
IRanges * 2.18.3 2019-09-24 [1] Bioconductor
iterators 1.0.12 2019-07-26 [1] CRAN (R 3.6.1)
jsonlite 1.6.1 2020-02-02 [1] CRAN (R 3.6.2)
KernSmooth 2.23-16 2019-10-15 [2] CRAN (R 3.6.2)
later 1.0.0 2019-10-04 [1] CRAN (R 3.6.1)
lattice 0.20-38 2018-11-04 [2] CRAN (R 3.6.2)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.1)
lifecycle 0.1.0 2019-08-01 [1] CRAN (R 3.6.1)
limma * 3.40.6 2019-07-26 [1] Bioconductor
lme4 1.1-21 2019-03-05 [1] CRAN (R 3.6.1)
locfit 1.5-9.1 2013-04-20 [1] CRAN (R 3.6.1)
lubridate 1.7.4 2018-04-11 [1] CRAN (R 3.6.1)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.1)
MASS 7.3-51.5 2019-12-20 [2] CRAN (R 3.6.2)
Matrix 1.2-18 2019-11-27 [1] CRAN (R 3.6.1)
matrixStats 0.55.0 2019-09-07 [1] CRAN (R 3.6.1)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.1)
mime 0.9 2020-02-04 [1] CRAN (R 3.6.2)
minqa 1.2.4 2014-10-09 [1] CRAN (R 3.6.1)
modelr 0.1.5 2019-08-08 [1] CRAN (R 3.6.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.1)
nlme 3.1-144 2020-02-06 [1] CRAN (R 3.6.2)
nloptr 1.2.1 2018-10-03 [1] CRAN (R 3.6.1)
packrat 0.5.0 2018-11-14 [1] CRAN (R 3.6.1)
pbkrtest 0.4-7 2017-03-15 [1] CRAN (R 3.6.1)
pillar 1.4.3 2019-12-20 [1] CRAN (R 3.6.2)
pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 3.6.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.1)
plyr 1.8.5 2019-12-10 [1] CRAN (R 3.6.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.2)
processx 3.4.2 2020-02-09 [1] CRAN (R 3.6.2)
progress 1.2.2 2019-05-16 [1] CRAN (R 3.6.1)
promises 1.1.0 2019-10-04 [1] CRAN (R 3.6.1)
ProtGenerics 1.16.0 2019-05-02 [1] Bioconductor
ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.2)
purrr * 0.3.3 2019-10-18 [1] CRAN (R 3.6.1)
R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.1)
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 3.6.1)
Rcpp 1.0.3 2019-11-08 [1] CRAN (R 3.6.1)
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 3.6.2)
readr * 1.3.1 2018-12-21 [1] CRAN (R 3.6.1)
readxl 1.3.1 2019-03-13 [1] CRAN (R 3.6.1)
remotes 2.1.1 2020-02-15 [1] CRAN (R 3.6.2)
reprex 0.3.0 2019-05-16 [1] CRAN (R 3.6.1)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.1)
rlang 0.4.4 2020-01-28 [1] CRAN (R 3.6.2)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.1)
Rsamtools 2.0.3 2019-10-10 [1] Bioconductor
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 3.6.2)
rstudioapi 0.11 2020-02-07 [1] CRAN (R 3.6.2)
rtracklayer 1.44.4 2019-09-06 [1] Bioconductor
rvest 0.3.5 2019-11-08 [1] CRAN (R 3.6.1)
S4Vectors * 0.22.1 2019-09-09 [1] Bioconductor
scales * 1.1.0 2019-11-18 [1] CRAN (R 3.6.1)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
shiny * 1.4.0 2019-10-10 [1] CRAN (R 3.6.1)
shinythemes * 1.1.2 2018-11-06 [1] CRAN (R 3.6.1)
stringi 1.4.4 2020-01-09 [1] CRAN (R 3.6.2)
stringr * 1.4.0 2019-02-10 [1] CRAN (R 3.6.1)
SummarizedExperiment 1.14.1 2019-07-31 [1] Bioconductor
testthat 2.3.1 2019-12-01 [1] CRAN (R 3.6.1)
tibble * 2.1.3 2019-06-06 [1] CRAN (R 3.6.1)
tidyr * 1.0.2 2020-01-24 [1] CRAN (R 3.6.2)
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 3.6.2)
tidyverse * 1.3.0 2019-11-21 [1] CRAN (R 3.6.1)
usethis 1.5.1 2019-07-04 [1] CRAN (R 3.6.1)
variancePartition * 1.14.1 2019-10-01 [1] Bioconductor
vctrs 0.2.2 2020-01-24 [1] CRAN (R 3.6.2)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.1)
XML 3.99-0.3 2020-01-20 [1] CRAN (R 3.6.2)
xml2 1.2.2 2019-08-09 [1] CRAN (R 3.6.1)
xtable 1.8-4 2019-04-21 [1] CRAN (R 3.6.2)
XVector 0.24.0 2019-05-02 [1] Bioconductor
yaml 2.2.1 2020-02-01 [1] CRAN (R 3.6.2)
zlibbioc 1.30.0 2019-05-02 [1] Bioconductor
Hi,
I don't know about version ENCODExplorer version 2.10 (which probably was in BioConductor release 2.9), but the function is definitely in ENCODExplorer 2.12.1, the one in the current BioConductor release (Bioc 2.10). Is there a reason why you can't switch to that one?
Cheers,
-Eric
Thanks Eric!
Using version 2.12.1 has fixed the issue.