Draft PR from Tina#242
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| # output_file <- file.path(output_dir, paste0(sample_id, "_allele_counts_consistent.tsv")) | ||
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| tryCatch({ |
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I think if you name the file .gz fwrite will automatically compress
| #' @param output_file Character. File for combined allele outputs | ||
| #' @param compress Logical. Whether to compress the output file (default: TRUE) | ||
| #' @return Character. Path to the output file | ||
| combine_allele_counts <- function(alleleCounts_RNA, |
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Discuss - could take union instead. Is this also used for summed? For summed I just rbind the two dataframes and sum the counts for the same cell-snp combo
| cntsubN(cntmat[[2]],sharedFeature,maxCB,seed)) | ||
| return(comb_cnt) | ||
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| if(add_suffix){ |
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Is this necessary? Why can't just append suffix to each matrix and combine?
| return(cnt) | ||
| } | ||
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| if(add_suffix){ |
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Why is this necessary for summed? seems repeated
Merge two function -> mode = intersect/union
| ```r | ||
| source(glue("{numbat_repo}/inst/bin/input_prep.R")) | ||
| combine_allele_counts( | ||
| alleleCounts_RNA = glue("${sample}/{sample}_rna_bin.rds"), |
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path names seems wrong
| ) | ||
| ``` | ||
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| #### Run Numbat with the --runMultiomeAsPaired tag |
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It's a bit confusing with all different running modes, can we make a separate tutorial for people who has joint multiome
Also need to clarify what paired mode is, I'm a bit unclear on this
| ``` | ||
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| #### Running Numbat Paired Mode: |
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Need some recommended parameters, etc.
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Also it still says paired
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Can we just give a run_numbat command instead?
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