findThresh: findThresh

In chris-mcginnis-ucsf/MULTI-seq: deMULTIplex is a software suite for MULTI-seq sample barcode FASTQ pre-processing and cell barcode classification.

findThresh

Description

'findThresh' summarizes the results of the quantile sweep performed during each round of the MULTI-seq sample classification workflow. Output is used to select the barcode-specific threshold used to classify cells during each round.

Usage

 findThresh(call.list) 

Arguments

call.list

List containing the singlet/doublet/negative classifications for each quantile threshold tested during a round of the MULTI-seq sample classification workflow.

Details

Requires the 'reshape2' R package.

Value

Returns a list containing (1) 'res': proportion of cells called as singlets (pSinglet), doublets (pDoublet), and negatives (pNegative) at each quantile tested, and (2) 'extrema': the local maxima for the pSinglet qunatile distribution.

Author(s)

Chris McGinnis

References

Hadley Wickham (2007). Reshaping Data with the reshape Package. Journal of Statistical Software, 21(12), 1-20.

Examples

  bar.table_sweep.list <- list()
  n <- 0
  for (q in seq(0.01, 0.99, by=0.02)) {
    print(q)
    n <- n + 1
    bar.table_sweep.list[[n]] <- classifyCells(data=barTable, q=q)
    names(bar.table_sweep.list)[n] <- paste("q=",q,sep="")
  }

  threshold.results1 <- findThresh(bar.table_sweep.list)
  round1.calls <- classifyCells(barTable, q=findQ(threshold.results1$res, threshold.results1$extrema))

chris-mcginnis-ucsf/MULTI-seq documentation built on Nov. 22, 2023, 8:24 p.m.