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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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Issue with BITFAM function #15

Open sugarglider12 opened 11 months ago

sugarglider12 commented 11 months ago

Hi, I was wondering if anyone has seen this issue before. After loading in my normalized seurat object, loading the relevant packages, I get the following error when running the BITFAM() command.

BITFAM_res <- BITFAM(data = normalized_data_matrix, species = "human", scATAC_obj = NA, ncores = parallel::detectCores()) 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: The following arguments are not used: drop Error in h(simpleError(msg, call)) : error in evaluating the argument 'i' in selecting a method for function '[': comparison (!=) is possible only for atomic and list types

Additionally, the preprocessing command produces a similar issue:

data_matrix_normalized <- BITFAM_preprocess(raw_data = d_matrix) Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'colSums': comparison (>) is possible only for atomic and list types

My R version is 4.3.0.

tobylanser commented 3 weeks ago

Hi @sugarglider12 . I also have this issue. Have you since fixed the problem?