ReadPISA

Source code

Description

Read feature count matrix generated by ‘PISA count’.

Usage

ReadPISA(
  mex_dir = NULL,
  prefix = NULL,
  suffix = NULL,
  cells = NULL,
  barcode.path = NULL,
  feature.path = NULL,
  matrix.path = NULL,
  peak.path = NULL,
  spliced.path = NULL,
  unspliced.path = NULL,
  spanning.path = NULL,
  use_10X = FALSE,
  spatial = FALSE
)

Arguments

mex_dir	Feature count outdir generated by ‘PISA count’.
prefix	Prefix to cell names.
suffix	Suffixed to cell names.
cells	Vector for candidate cells. If not set, will read all cells.
barcode.path	Manually specify barcode path in MEX directory.
feature.path	Manually specify feature path in MEX directory.
matrix.path	Manually specify matrix path in MEX directory.
peak.path	Manually specific peak path (if feature is a region) in MEX directory.
spliced.path	Manually specific spliced matrix path in MEX directory. The spliced, unspliced and spanning read count matrix generated by ‘PISA count -velo’.
unspliced.path	Manually specific unspliced matrix path.
spanning.path	Manually specific spanning matrix path.
use_10X	Set TRUE if feature name in the second column of feature file.
spatial	Set TRUE if barcode is coordinate of bin. Will combine x and y coordinate into bin name “x_y”.

Value

Returns a sparse matrix of feature counts or a list of spliced, unspliced, and spanning reads sparse matrix.