create_report: create_report

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

create_report

Description

create an HTML report using data generated by proprocessing step.

Usage

create_report(
  sample_name,
  outdir,
  r1 = "NA",
  r2 = "NA",
  outfq = "NA",
  read_structure = list(bs1 = 0, bl1 = 0, bs2 = 0, bl2 = 0, us = 0, ul = 0),
  filter_settings = list(rmlow = TRUE, rmN = TRUE, minq = 20, numbq = 2),
  align_bam = "NA",
  genome_index = "NA",
  map_bam = "NA",
  exon_anno = "NA",
  stnd = TRUE,
  fix_chr = FALSE,
  barcode_anno = "NA",
  max_mis = 1,
  UMI_cor = 1,
  gene_fl = FALSE,
  organism,
  gene_id_type
)

Arguments

sample_name	sample name
outdir	output folder
r1	file path of read1
r2	file path of read2 default to be NULL
outfq	file path of the output of sc_trim_barcode
read_structure	a list contains read structure configuration. For more help see '?sc_trim_barcode'
filter_settings	a list contains read filter settings for more help see '?sc_trim_barcode'
align_bam	the aligned bam file
genome_index	genome index used for alignment
map_bam	the mapped bam file
exon_anno	the gff exon annotation used. Can have multiple files
stnd	whether to perform strand specific mapping
fix_chr	add 'chr' to chromosome names, fix inconsistent names.
barcode_anno	cell barcode annotation file path.
max_mis	maximum mismatch allowed in barcode. Default to be 1
UMI_cor	correct UMI sequence error: 0 means no correction, 1 means simple correction and merge UMI with distance 1.
gene_fl	whether to remove low abundant gene count. Low abundant is defined as only one copy of one UMI for this gene
organism	the organism of the data. List of possible names can be retrieved using the function 'listDatasets'from 'biomaRt' package. (i.e 'mmusculus_gene_ensembl' or 'hsapiens_gene_ensembl')
gene_id_type	gene id type of the data A possible list of ids can be retrieved using the function 'listAttributes' from 'biomaRt' package. the commonly used id types are 'external_gene_name', 'ensembl_gene_id' or 'entrezgene'

Value

no return

Examples

## Not run: 
create_report(sample_name="sample_001",
       outdir="output_dir_of_scPipe",
       r1="read1.fq",
       r2="read2.fq",
       outfq="trim.fq",
       read_structure=list(bs1=-1, bl1=2, bs2=6, bl2=8, us=0, ul=6),
       filter_settings=list(rmlow=TRUE, rmN=TRUE, minq=20, numbq=2),
       align_bam="align.bam",
       genome_index="mouse.index",
       map_bam="aligned.mapped.bam",
       exon_anno="exon_anno.gff3",
       stnd=TRUE,
       fix_chr=FALSE,
       barcode_anno="cell_barcode.csv",
       max_mis=1,
       UMI_cor=1,
       gene_fl=FALSE,
       organism="mmusculus_gene_ensembl",
       gene_id_type="ensembl_gene_id")

## End(Not run)

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