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jaleesr / BITFAM

BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.
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interseted_TFs #9

Closed jziggles closed 1 year ago

jziggles commented 1 year ago

Hello - I have been using BITFAM and it has been great, thanks. I am working on human data and trying to use the interseted TF option though this does not seem to be working currently - below is the line of code. Please let me know thanks.

BITFAM_res <- BITFAM(data = data_matrix_normalized, interseted_TF = c("IRF3", "IRF7"), species = "human", scATAC_obj = NA, ncores = parallel::detectCores())

sgao30 commented 1 year ago

Hi, Thank you for using our tool! What is the error you have? Currently, IRF7 is not in the TF ChIP-seq database. So you cannot do the inference on IRF7. If you have IRF7 ChIP-seq data or IRF7 target gene list, you can put it into the extdata folder. Please let me know if you need more help!

jziggles commented 1 year ago

Hi - thank you for the response. Answers below.

This is the initial error:

Error in BITFAM(data = data_matrix_normalized, interseted_TF = c("IRF3", : unused argument (scATAC_obj = NA)

After removing scATAC_obj = NA and rerunning:

Error in if (is.na(interseted_TF)) { : the condition has length > 1

I suspect because of what you said about IRF7 - it runs after removing IRF7 - thanks!

liezeltamon commented 5 months ago

Hi @sgao30, I think the above problem is related to this issue #16 I posted last year. I guess the checking for NA in interseted_TF throws an error if interseted_TF is a vector of elements. Would be nice to fix the checking of NAs so we can input multiple TFs of interest.

Thank you!