scraps_to_matrix: Read scraps output from umi_tools to sparseMatrix
In rnabioco/scrapR: scraps output import and processing in R

scraps_to_matrix

R Documentation

Read scraps output from umi_tools to sparseMatrix

Description

Read scraps output from umi_tools to sparseMatrix

Usage

scraps_to_matrix(
  file,
  n_min = 5,
  gene_min = 5,
  alt_only = FALSE,
  filter_low = TRUE,
  cell_ids = NULL,
  types = "3'UTR",
  types2 = NULL,
  pf = NULL
)

Arguments

`file`	scraps output table containing
`n_min`	minimum number of observations for a site to be kept
`gene_min`	minimum number of observations for gene to be kept
`alt_only`	if TRUE, only keep genes with alternative polyA sites
`filter_low`	if TRUE, remove low genes and cell ids, if FALSE, set to -1
`cell_ids`	if given, use only these cell barcodes, and fill in empty ones
`types`	filter to only these types of PA sites, set to NULL to use all
`types2`	another filter to only these types of PA sites, set to NULL to use all
`pf`	data.frame with SAF first column and position factor by gene, calculated by `parse_saf_pf`