brtMatch_10x_bc: brtMatch_10x_bc

In c57bl/Brt:

brtMatch_10x_bc

Description

brtMatch_10x_bc will match and the counts the umi grouped by 10x barcode and barcodes provided from library made from 10x cdna. The reads2 contains the cell barcode and the reads1 contains the target gene information

Usage

brtMatch_10x_bc(
  path,
  rvBarcode_pattern,
  quality_cutoff = 25,
  cellBelow = 2,
  rvBelow = 2,
  blockSize = 2e+06,
  rvBarcode_max_mismatch = 0,
  rvBarcode_roi = NULL,
  rvBarcode_cutoff = 3,
  cell_cutoff = 3,
  ncore = 1,
  rvBarcode_reference = NULL,
  cell_reference = NULL,
  total = NULL
)

Arguments

rvBarcode_pattern	A character or character vector
quality_cutoff	a integer specify low quality string
cellBelow	a integer, the read will be drooped if the number of low quality string in cell barcode region exceeds it.
rvBelow	a integer, the read will be drooped if the number of low quality string in rvbarcode region(the region could be future modified by rvBarcode_roi) exceeds it.
blockSize	a numeric value specify the number of reads to be load in recursive loading
rvBarcode_max_mismatch	a integer, the pattern match were performed by biostring::vmatchpattern and the rvBarcode_max_mismatch control the max_mismatch parameter
ncore	a numeric value specify the cores used in time consuming steps
rvBarcode_reference	a character vector provide the white list of rvBarcode, the unmatched barcode will be droped
cell_reference	a character vector provide the white list of cell barcode, the unmatched cell will be droped
rvBarcode_row	a numeric vector to extract pure barcode from barcode region
seq_library	a character,'cdna'/'10x'

Value

a tibble with colnames cell,bc counts

c57bl/Brt documentation built on May 20, 2022, 8:45 p.m.