could not find function "filter_cells_and_genes"

[WANGW-z]

I hope this message finds you well. I am currently encountering some difficulties while running a program, and I would greatly appreciate your assistance in resolving these issues.

library(SingCellaR)

setwd("/mnt/sdc/wwDatas/singleCells/GSE116106/SRR7405851_res/SingCellaR_res") data_matrices_dir<-"/mnt/sdc/wwDatas/singleCells/GSE116106/SRR7405851_res/Solo.out/Gene/filtered" eFL_1<-new("SingCellaR") eFL_1@dir_path_10x_matrix<-data_matrices_dir eFL_1@sample_uniq_id<-"eFL_1" load_matrices_from_cellranger(eFL_1,cellranger.version = 3)# [1] "The sparse matrix is created." eFL_1 An object of class SingCellaR with a matrix of : 70611 genes across 5491 samples. process_cells_annotation(eFL_1, mito_genes_start_with="MT-") [1] "List of mitochondrial genes:" [1] "MT-TF" "MT-RNR1" "MT-TV" "MT-RNR2" "MT-TL1" "MT-ND1" "MT-TI"
[8] "MT-TQ" "MT-TM" "MT-ND2" "MT-TW" "MT-TA" "MT-TN" "MT-TC"
[15] "MT-TY" "MT-CO1" "MT-TS1" "MT-TD" "MT-CO2" "MT-TK" "MT-ATP8" [22] "MT-ATP6" "MT-CO3" "MT-TG" "MT-ND3" "MT-TR" "MT-ND4L" "MT-ND4" [29] "MT-TH" "MT-TS2" "MT-TL2" "MT-ND5" "MT-ND6" "MT-TE" "MT-CYB" [36] "MT-TT" "MT-TP"
[1] "The meta data is processed." filter_cells_and_genes(eFL_1,

• min_UMIs=1000,
• max_UMIs=50000,
• min_detected_genes=500,
• max_detected_genes=6000,
• max_percent_mito=10,
• genes_with_expressing_cells = 10,
• isRemovedDoublets = FALSE) Error in filter_cells_and_genes(eFL_1, min_UMIs = 1000, max_UMIs = 50000, : could not find function "filter_cells_and_genes" @supatt-lab

[supatt-lab]

Hi,

In R terminal, please try:

?filter_cells_and_genes

Please copy and paste the above function name and see if that works. I think there was something wrong when you copied the function name. In particular, there was something wrong with "fil".

Maybe simply type it in -> filter_cells_and_genes

I hope this helps!

Best, Supat

[WANGW-z]

Dear Supat,

I hope this message finds you well.

Thank you very much for your prompt response to my email. During my attempts to run the script afterwards, I discovered that the error I encountered was due to copying and pasting commands directly from the PDF file. I found that if I copied and pasted the scripts from the web version of the tutorial, I did not encounter any issues.

I truly appreciate your assistance in this matter. Wishing you all the best in your work!

Best regards,

At 2024-09-04 02:17:08, "Supat Thongjuea" @.***> wrote:

Hi,

In R terminal, please try:

?filter_cells_and_genes

Please copy and paste the above function name and see if that works. I think there was something wrong when you copied the function name. In particular, there was something wrong with "fil".

Maybe simply type it in -> filter_cells_and_genes

I hope this helps!

Best, Supat

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

--

WANG, Wen, Ph.D.

Bioinformatic researcher

Staff member, Beijing Institute of Ophthalmology (BIO)

Beijing Tongren Hospital, Capital Medical University

E-mail: @.***