create_report {scPipe} | R Documentation

## 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 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'

### 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)

[Package scPipe version 1.2.1 Index]