Error running inferCNV::run

[swati gupta]

Hi,

I am trying to find tumor cells in my dataset of epithelial cells. I have labelled the wild type condition cells as my reference (ob1). 

When running the infercnv:: run command (whole code below):

newobj<-readRDS('integrated_epi.rds')
Idents(newobj)<-'dataset'
DefaultAssay(newobj)<-'RNA'
counts_matrix <- GetAssayData(newobj,slot ="counts")
ann<-ne...@meta.data[,"dataset",drop=FALSE]
infercnv_obj = CreateInfercnvObject(raw_counts_matrix=counts_matrix,
                                    annotations_file=ann,
                                   gene_order_file="gene_orderfile.txt",
                                    delim="\t",
                                    ref_group_names=c("ob1"))

# perform infercnv operations to reveal cnv signal
infercnv_obj = infercnv::run(infercnv_obj,
                             cutoff=0.1,  # use 1 for smart-seq, 0.1 for 10x-genomics## since already processed count matrix setting to 0
                             out_dir="infercnv_out",  # dir is auto-created for storing outputs
                             denoise=T,
                             HMM=T
)

I am getting the following error:

STEP 15: computing tumor subclusters via leiden INFO [2023-12-03 16:19:37] define_signif_tumor_subclusters(p_val=0.1 INFO [2023-12-03 16:19:37] define_signif_tumor_subclusters(), tumor: ob2 Warning: Data is of class matrix. Coercing to dgCMatrix. Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Warning: No layers found matching search pattern provided Error in `ScaleData()`: ! No layer matching pattern 'data' found. Please run NormalizeData and retry

My seurat object was normalized and scaled and had the data slot in RNA assay. But I cant see any 'data' in infercnv_obj. Please advice on how to proceed.

[Alice Dong]

Hi, 

I have the same error. Did any of you figure out the reason or have any suggestions please?

[cgeo...@broadinstitute.org]

Hi,

Version 1.18.1 of infercnv that is available on BioConductor should have this issue fixed, so simply updating your install should allow the run to keep going.

Regards,

Christophe.

[Alice Dong]

Thanks! The error was fixed!

[swati gupta]

Hi,

Thanks a lot.

This worked for me as well. 

Can you also point me to how I can understand the results and use them to infer the tumor cells from the sample?

Swati