create_report: create_report
In scPipe: pipeline for single cell RNA-seq data analysis

Description Usage Arguments Value Examples

create an HTML report using data generated by proprocessing step.

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)

`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 inconsistant 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'

no return

## 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)