TssEnrichmentFromFrags: Calculate tss enrichment score from 10xscATAC...

Description Usage Arguments Value Examples

View source: R/TssEnrichmentFromFrags.R

Description

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

Usage

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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)

Arguments

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

Value

A dataframe with two columns: cells and the tss_score.

Examples

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## 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)

crazyhottommy/scATACutils documentation built on June 15, 2020, 9:31 p.m.