PeteHaitch
commented
7 years ago Hi Divy,
Linear single bracked subsetting
The following works for me:
suppressPackageStartupMessages(library(DelayedArray))
set.seed(666)
a <- array(runif(1500000), dim=c(10000, 30, 5))
A <- DelayedArray(a)
A[which(A <= 1e-5)]
#> [1] 3.061723e-06 8.459203e-06 2.210494e-06 9.671785e-07 9.246171e-06
#> [6] 4.540198e-06 1.884997e-06 9.980286e-06 9.364448e-06 8.054543e-06
#> [11] 8.265488e-06 7.253839e-06 4.062895e-07Session info
``` r devtools::session_info() #> Session info ------------------------------------------------------------- #> setting value #> version R version 3.4.1 (2017-06-30) #> system x86_64, darwin15.6.0 #> ui X11 #> language (EN) #> collate en_AU.UTF-8 #> tz America/New_York #> date 2017-09-25 #> Packages ----------------------------------------------------------------- #> package * version date source #> backports 1.1.0 2017-05-22 CRAN (R 3.4.0) #> base * 3.4.1 2017-07-07 local #> BiocGenerics * 0.23.1 2017-09-05 Bioconductor #> compiler 3.4.1 2017-07-07 local #> datasets * 3.4.1 2017-07-07 local #> DelayedArray * 0.3.19 2017-07-28 Bioconductor #> devtools 1.13.3 2017-08-02 CRAN (R 3.4.1) #> digest 0.6.12 2017-01-27 CRAN (R 3.4.0) #> evaluate 0.10.1 2017-06-24 CRAN (R 3.4.0) #> graphics * 3.4.1 2017-07-07 local #> grDevices * 3.4.1 2017-07-07 local #> htmltools 0.3.6 2017-04-28 CRAN (R 3.4.0) #> IRanges * 2.11.16 2017-09-15 Bioconductor #> knitr 1.17 2017-08-10 CRAN (R 3.4.1) #> magrittr 1.5 2014-11-22 CRAN (R 3.4.0) #> matrixStats * 0.52.2 2017-04-14 CRAN (R 3.4.0) #> memoise 1.1.0 2017-05-26 Github (hadley/memoise@e372cde) #> methods * 3.4.1 2017-07-07 local #> parallel * 3.4.1 2017-07-07 local #> Rcpp 0.12.12 2017-07-15 CRAN (R 3.4.1) #> rmarkdown 1.6 2017-06-15 CRAN (R 3.4.0) #> rprojroot 1.2 2017-01-16 CRAN (R 3.4.0) #> S4Vectors * 0.15.8 2017-09-14 Bioconductor #> stats * 3.4.1 2017-07-07 local #> stats4 * 3.4.1 2017-07-07 local #> stringi 1.1.5 2017-04-07 CRAN (R 3.4.0) #> stringr 1.2.0 2017-02-18 CRAN (R 3.4.0) #> tools 3.4.1 2017-07-07 local #> utils * 3.4.1 2017-07-07 local #> withr 2.0.0 2017-07-28 CRAN (R 3.4.1) #> yaml 2.1.14 2016-11-12 CRAN (R 3.4.0) ```What is the output when you run the above code in a new session? And what is the output of sessionInfo() or devtools::session_info()?
Subassignment
DelayedArray objects do not currently support subassignment ([<- or [[<-); this is documented in the final sentence of the 'Subsetting' section of the help page?DelayedArray::DelayedArray
Cheers, Pete
hpages
divy-kangeyan
Hi, I am using DelayedArray package to process some sequencing data. In the manual it says DelayedArray object can be subsetted by a logical DelayedArray object. So I tried some of the examples in the manual.
Linear single bracket subsetting:
A[which(A <= 1e-5)]Subassignment:
A[A < 0.2] <- NAwhere A is a delayedArray.Linear single bracket subsetting didn't work and I got this error
Error in which(A <= 1e-05) : argument to 'which' is not logical, I am guessing which function is not recognizing logical delayedArray object as an acceptable logical object.For Subassignment, I am getting the following error
Error in A[A < 0.2] <- NA : object of type 'S4' is not subsettableAny idea why this is happening? My main intent was to subset the DelayedArray, so is it possible in this case?
Thank you, Divy