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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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error during HMM prediction #547

Open veramazzara opened 1 year ago

veramazzara commented 1 year ago

Hi GeorgescuC, thank you for this useful tool! I am working with R version 4.2.3 and infercnv 1.14.2 but I can't be able to obtain prediction with HMM model.

I'm working without reference cells

infercnv_obj_default = infercnv::run( infercnv_object_example, cutoff=0.1, out_dir=getwd(), cluster_by_groups=TRUE, plot_steps=FALSE, denoise=TRUE, HMM=TRUE, HMM_type=c("i3"), analysis_mode="subclusters",

no_prelim_plot=TRUE,

png_res=300, num_threads = 4 )

I obtained this error:

STEP 17: HMM-based CNV prediction

INFO [2023-05-25 21:37:30] i3HMM_predict_CNV_via_HMM_on_tumor_subclusters(i3_p_val=0.05, use_KS=FALSE) INFO [2023-05-25 21:37:31] determine mean delta (sigma: NA, p=0.05) -> NA mean_delta: NA, at sigma: NA, and pval: 0.05 WARN [2023-05-25 21:37:31] get_HoneyBADGER_setGexpDev:: k_cells must be at least 2, setting to 2 Error in seq.default(0, gexp.sd, gexp.sd/10) : 'to' must be a finite number

Is it possible to apply HMM model without reference cells? If yes, how can fix this issue?

Thank you so much.

Vera

GeorgescuC commented 1 year ago

Hi @veramazzara ,

I have pushed a commit to allow the i3 model to work by taking its parameters from all observations when no references are provided. Just keep in mind that when no references are provided, the average of all observations is used as the baseline to which everything is compared, so results may be flipped to reality depending on the proportion of healthy/tumor (with a given cnv) cells. To get the update, you will need to update using the code on github with:

library("devtools")
devtools::install_github("broadinstitute/infercnv")

Regards, Christophe.

veramazzara commented 1 year ago

Hi Christophe, my apologies for my slow response. Thank you very much for this further commit; now I can run HMM prediction! And thank you for alerting me about the results's interpretation without the reference.

Regards,

Vera