create_report: create_report

Description Usage Arguments Value Examples

View source: R/sc_workflow.R

Description

create an HTML report using data generated by proprocessing step.

Usage

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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

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## 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)

scPipe documentation built on Nov. 8, 2020, 8:28 p.m.