Seurat: PercentageFeatureSet function not found

[0x644BE25]

The Seurat 3.0 Guided Clustering tutorial uses PercentageFeatureSet(), but when I attempt to call it I get the error
Error in PercentageFeatureSet(object = data, pattern = "MT-") : could not find function "PercentageFeatureSet"

Here's the output from sessionInfo(), confirming that I am using Seurat 3

R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /n/apps/CentOS7/install/r-3.5.2/lib64/R/lib/libRblas.so
LAPACK: /n/apps/CentOS7/install/r-3.5.2/lib64/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] dplyr_0.8.0.1 knitr_1.21 shiny_1.2.0 pryr_0.1.4 Seurat_3.0.0.9000

loaded via a namespace (and not attached):
[1] nlme_3.1-137 tsne_0.1-3 bitops_1.0-6 RColorBrewer_1.1-2 httr_1.4.0 tools_3.5.2 R6_2.4.0
[8] irlba_2.3.3 KernSmooth_2.23-15 lazyeval_0.2.1 colorspace_1.4-0 withr_2.1.2 npsurv_0.4-0 tidyselect_0.2.5
[15] compiler_3.5.2 Cairo_1.5-9 plotly_4.8.0 labeling_0.3 caTools_1.17.1.1 scales_1.0.0 lmtest_0.9-36
[22] ggridges_0.5.1 pbapply_1.4-0 stringr_1.4.0 digest_0.6.18 rmarkdown_1.11 R.utils_2.8.0 pkgconfig_2.0.2
[29] htmltools_0.3.6 bibtex_0.4.2 htmlwidgets_1.3 rlang_0.3.1 rstudioapi_0.9.0 zoo_1.8-4 jsonlite_1.6
[36] ica_1.0-2 gtools_3.8.1 R.oo_1.22.0 magrittr_1.5 Matrix_1.2-15 Rcpp_1.0.0 munsell_0.5.0
[43] ape_5.2 reticulate_1.10 R.methodsS3_1.7.1 stringi_1.3.1 yaml_2.2.0 gbRd_0.4-11 MASS_7.3-51.1
[50] gplots_3.0.1.1 Rtsne_0.15 plyr_1.8.4 grid_3.5.2 parallel_3.5.2 gdata_2.18.0 listenv_0.7.0
[57] promises_1.0.1 ggrepel_0.8.0 crayon_1.3.4 lattice_0.20-38 cowplot_0.9.4 splines_3.5.2 SDMTools_1.1-221
[64] pillar_1.3.1 igraph_1.2.4 future.apply_1.1.0 codetools_0.2-16 glue_1.3.0 evaluate_0.13 lsei_1.2-0
[71] metap_1.1 data.table_1.12.0 png_0.1-7 httpuv_1.4.5.1 Rdpack_0.10-1 gtable_0.2.0 RANN_2.6.1
[78] purrr_0.3.0 tidyr_0.8.2 future_1.11.1.1 assertthat_0.2.0 ggplot2_3.1.0 xfun_0.4 rsvd_1.0.0
[85] mime_0.6 xtable_1.8-3 later_0.8.0 rsconnect_0.8.13 survival_2.43-3 viridisLite_0.3.0 tibble_2.0.1
[92] cluster_2.0.7-1 globals_0.12.4 fitdistrplus_1.0-14 ROCR_1.0-7`

Thanks!

[satijalab]

We've just added this function very recently, so please make sure you have the absolute latest Seurat v3 install

[GHAStVHenry]

has it been committed yet to the public release/3.0 yet, because it is still not there.

[satijalab]

https://github.com/satijalab/seurat/blob/9e1a63ab2757170d8214543b6099d3491d7b13fe/R/utilities.R#L877-L923

[piepertc]

I copied and pasted the above PercentageFeatureSet function and my R Studio is not happy with the "%| |%" notation in the function:

Error in assay %||% DefaultAssay(object = object) :
could not find function "%||%"

Any advice on this? Sorry if this is particularly simple; I'm pretty new to R.

Thanks in advance!

[0x644BE25]

@piepertc If you install the very latest Seurat that requires compiling, it appears to have PercentageFeatureSet() working fine. If you'd rather not update just yet, it looks like you're missing a tiny helper function hidden elsewhere in the larger utilities.R file. Try adding

# Set a default value if an object is null
#
# @param lhs An object to set if it's null
# @param rhs The value to provide if x is null
#
# @return rhs if lhs is null, else lhs
#
# @author Hadley Wickham
# @references https://adv-r.hadley.nz/functions.html#missing-arguments
#
`%||%` <- function(lhs, rhs) {
  if (!is.null(x = lhs)) {
    return(lhs)
  } else {
    return(rhs)
  }
}

to your code and see if that fixes it.

[piepertc]

@0x644BE25 That does seem to have circumvented the %||% issue, but now a new problem is arising with the PercentFeatureSet Function:

Error in colSums(x = GetAssayData(object = object, slot = "counts")[features, :
'x' must be an array of at least two dimensions

I find that line in the PercentFeatureSet code but I am not entirely sure what changes to make.

I really appreciate your help!

Also of note, I believe I am using the most recent version of Seurat:

packageVersion("Seurat")
[1] ‘3.0.0.9000’

is this correct?

[RicedeKrispy]

For what it's worth, I'm having the same "Error in PercentageFeatureSet(rpe, pattern = "^MT-") :
could not find function "PercentageFeatureSet" issue, version 3.0.0.9 updated just now.

[andrewwbutler]

The current version of Seurat is 3.0.1. Please install that version and try again

[naomi-croft]

Hi, I have Seurat version ‘3.0.2’

I still get the error message "could not find function "PercentageFeatureSet" "

Any advice?

[naomi-croft]

I restarted R and that seems to have solved the problem. However, as I have now updated the Seurat package, the following features can no longer be found in the seurat object- nGene and nUMI

Have they been renamed?
Thanks for helping!

[asebastianyague]

Seems that loading the Matrix package solved the issue for me: library('Matrix')