garnett_check_markers not working for Fly
Closed this issue · 4 comments
Describe the bug
Hi,
I'm trying to use Garnett for Fly dataset. Unfortunately, check_markers
is failing because it does not allow for markers to have special characters while in Fly we do find some that have: e.g.: E(spl)m8-HLH
To Reproduce
marker_check <- check_markers(cds = cds,
"Garnett_markers.txt",
db = get(x = "org.Dm.eg.db"),
cds_gene_id_type = "SYMBOL",
marker_file_gene_id_type = "SYMBOL",
propogate_markers = TRUE,
use_tf_idf = TRUE,
classifier_gene_id_type = "SYMBOL")
Expected behavior
/
Screenshots
Here is a screenshot of the bug I get:
Additional context
Here is my R session info:
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK:
Random number generation:
RNG: Mersenne-Twister
Normal: Inversion
Sample: Rounding
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] splines stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] Seurat_3.1.4 garnett_0.1.14 monocle_2.14.0 DDRTree_0.1.5
[5] irlba_2.3.3 VGAM_1.1-2 ggplot2_3.2.1 Matrix_1.2-18
[9] org.Dm.eg.db_3.10.0 AnnotationDbi_1.48.0 monocle3_0.2.1 SingleCellExperiment_1.8.0
[13] SummarizedExperiment_1.16.1 DelayedArray_0.12.2 BiocParallel_1.20.1 matrixStats_0.55.0
[17] GenomicRanges_1.38.0 GenomeInfoDb_1.22.0 IRanges_2.20.2 S4Vectors_0.24.3
[21] Biobase_2.46.0 BiocGenerics_0.32.0
Hi @dweemx ,
Can you give the new branch I've just made a try with your data? You can install using
devtools::install_github("cole-trapnell-lab/garnett", ref="fly_genes")
If it works, then I'll merge it back into master - I don't have any example fly data to play with!
Thanks, I'll give it a try and let you know
Just tested your patch version fly_genes
and its working ! 👍
Great, thanks for testing! Just pulled to master!