TssEnrichmentFromFrags: Calculate tss enrichment score from 10xscATAC...
In crazyhottommy/scATACutils: What the Package Does (One Line, Title Case)

Description Usage Arguments Value Examples

The memory usuage is not high (~5G), but takes ~2hours for 5000 cells.

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TssEnrichmentFromFrags(frag_gz_file, txs, flank = 1000, endFlank = 100,
  highest_tss_flank = 50, smooth = 50, strand.aware = TRUE,
  workers = 1, barcodeList = NULL)

`frag_gz_file`	fragment.tsv.gz file from 10x cellranger-atac output or anyother tool but in the same format.
`txs`	a txdb object
`flank`	flanking bp of tss (upstream and downstream)
`endFlank`	bp end flanks of flank for local noise control ——-flank———flank——- —————-\|—————– —————tss—————- endFlank—————–endFlank
`highest_tss_flank`	bp flanking tss windown for choosing the highest tss score. The highest tss enrichment score is not always exactly at tss.
`smooth`	window size to smooth
`strand.aware`	consider tss strandness when calculating
`barcodeList`	A vector of valid barcodes

A dataframe with two columns: cells and the tss_score.

## Not run: 
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
library(dplyr); library(readr); library(BiocParallel)
txs<- TxDb.Hsapiens.UCSC.hg19.knownGene
scores<- TssEnrichmentFromFrags("fragment.tsv.gz", txs = txs)

## End(Not run)