create_report {scPipe} | R Documentation |
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 |
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)