sc_atac_feature_counting: generating the feature by cell matrix

In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing

generating the feature by cell matrix

Description

feature matrix is created using a given demultiplexed BAM file and a selected feature type

Usage

sc_atac_feature_counting(
  fragment_file,
  feature_input = NULL,
  bam_tags = list(bc = "CB", mb = "OX"),
  feature_type = "peak",
  organism = "hg38",
  cell_calling = "filter",
  sample_name = "",
  genome_size = NULL,
  promoters_file = NULL,
  tss_file = NULL,
  enhs_file = NULL,
  gene_anno_file = NULL,
  pheno_data = NULL,
  bin_size = NULL,
  yieldsize = 1e+06,
  n_filter_cell_counts = 200,
  n_filter_feature_counts = 10,
  exclude_regions = FALSE,
  excluded_regions_filename = NULL,
  output_folder = NULL,
  fix_chr = "none",
  lower = NULL,
  min_uniq_frags = 3000,
  max_uniq_frags = 50000,
  min_frac_peak = 0.3,
  min_frac_tss = 0,
  min_frac_enhancer = 0,
  min_frac_promoter = 0.1,
  max_frac_mito = 0.15,
  create_report = FALSE
)

Arguments

fragment_file	The fragment file
feature_input	The feature input data e.g. the .narrowPeak file for peaks of a bed file format
bam_tags	The BAM tags
feature_type	The type of feature
organism	The organism type (contains hg19, hg38, mm10)
cell_calling	The desired cell calling method; either cellranger, emptydrops or filter.
sample_name	The sample name to identify which is the data is analysed for.
genome_size	The size of the genome (used for the cellranger cell calling method)
promoters_file	The path of the promoter annotation file (if the specified organism isn't recognised).
tss_file	The path of the tss annotation file (if the specified organism isn't recognised).
enhs_file	The path of the enhs annotation file (if the specified organism isn't recognised).
gene_anno_file	The path of the gene annotation file (gtf or gff3 format).
pheno_data	The phenotypic data as a data frame
bin_size	The size of the bins
yieldsize	The yield size
n_filter_cell_counts	An integer value to filter the feature matrix on the number of reads per cell (default = 200)
n_filter_feature_counts	An integer value to filter the feature matrix on the number of reads per feature (default = 10).
exclude_regions	Whether or not the regions (specified in the file) should be excluded
excluded_regions_filename	The filename of the file containing the regions to be excluded
output_folder	The output folder
fix_chr	Whether chr should be fixed or not
lower	the lower threshold for the data if using the emptydrops function for cell calling
min_uniq_frags	The minimum number of required unique fragments required for a cell (used for filter cell calling)
max_uniq_frags	The maximum number of required unique fragments required for a cell (used for filter cell calling)
min_frac_peak	The minimum proportion of fragments in a cell to overlap with a peak (used for filter cell calling)
min_frac_tss	The minimum proportion of fragments in a cell to overlap with a tss (used for filter cell calling)
min_frac_enhancer	The minimum proportion of fragments in a cell to overlap with a enhancer sequence (used for filter cell calling)
min_frac_promoter	The minimum proportion of fragments in a cell to overlap with a promoter sequence (used for filter cell calling)
max_frac_mito	The maximum proportion of fragments in a cell that are mitochondrial (used for filter cell calling)
create_report	Logical value to say whether to create the report or not (default = TRUE).

Value

None (invisible 'NULL')

Examples

## Not run: 
sc_atac_feature_counting(
   fragment_file = fragment_file,
   cell_calling = "filter",
   exclude_regions = TRUE,
   feature_input = feature_file)

## End(Not run)    

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.