collapse_intron_counts: Merge counts from intron reads with corresponding cDNA reads

In AlexsLemonade/scpcaTools: Single cell data tools for ScPCA

Merge counts from intron reads with corresponding cDNA reads

Description

Merge counts from intron reads with corresponding cDNA reads

Usage

collapse_intron_counts(
  counts,
  which_counts = c("spliced", "total", "unspliced")
)

Arguments

counts	Counts matrix with rownames corresponding to gene names and colnames corresponding to cell barcodes. Can be a counts matrix with intron counts specified by -I or an alevin-fry "USA" matrix, with intron counts marked by "-U" and ambiguous counts "-A".
which_counts	Which type of counts should be included: Only counts aligned to spliced cDNA ("spliced") or all spliced and unspliced cDNA ("unspliced" or "total"). Ambiguous counts in USA mode are always included. Default is "spliced".

Value

unfiltered gene x cell counts matrix

Examples

## Not run: 

# only keep counts from spliced cDNA in final counts matrix
collapse_intron_counts(counts,
  which_counts = "spliced"
)

# include unspliced cDNA in final counts matrix
collapse_intron_counts(counts,
  which_counts = "total"
)

## End(Not run)

AlexsLemonade/scpcaTools documentation built on July 12, 2024, 8:34 a.m.