quality_report: Generate general and individualized reports

View source: R/quality_report.R

quality_reportR Documentation

Generate general and individualized reports

Description

This function uses the other functions already described to create a HTML report based on sequencing quality. Besides the HTML reports, it also creates fasta files with all the sequences and individualized sequences, in addition to a csv file with the quality scores and sequences considered as good quality.

Usage

quality_report(
  folder_sequences = "path/to/sanger_sequences",
  outputfile = "QC_report.html",
  output_dir = "test/",
  processors = NULL,
  folder_path_fcs = NULL,
  plot_chromatogram = FALSE,
  raw_length = 343,
  trim_start = 65,
  trim_finish = 400,
  trimmed_mean_quality = 30,
  compensation = TRUE,
  plate_wells = "96",
  probe1 = "Pre.F",
  probe2 = "Post.F",
  posvalue_probe1 = 600,
  posvalue_probe2 = 400,
  cdr3_start = 100,
  cdr3_end = 150
)

Arguments

folder_sequences

Full file directory for searching all ab1 files in a recursive search method. It includes all files in subfolders

outputfile

Output file name for the report generation

output_dir

Output directory for all the different output files that are generated during the report

processors

Number of processors to use, you can set to NULL to detect automatically all available processors

folder_path_fcs

Full file directory for searching all flow cytometry index files, files with .fcs extensions, in a recursive search method

plot_chromatogram

Logical argument, TRUE or FALSE, to indicate if chromatograms should be plotted or not. Default is FALSE

raw_length

Minimum sequence length for filtering. Default is 343 for B cell receptors

trim_start

Starting position where the sequence should start to have a good base call accuracy. Default is 65 for B cell receptors

trim_finish

Last position where the sequence should have a good base call accuracy. Default is 400 for B cell receptors

trimmed_mean_quality

Minimum Phred quality score expected for an average sequence. Default is 30, which means average of 99.9% base call accuracy

compensation

Logical argument, TRUE or FALSE, to indicate if the index files were compensated or not. If TRUE, it will apply its compensation prior assigning specificities

plate_wells

Type of plate used for single-cell sorting. eg. "96" or "384"

probe1

Name of the first channel used for the probe or the custom name assigned to the channel in the index file. eg. "FSC.A", "FSC.H", "SSC.A","DsRed.A", "PE.Cy5_5.A", "PE.Cy7.A","BV650.A", "BV711.A","Alexa.Fluor.700.A" "APC.Cy7.A","PerCP.Cy5.5.A","Time"

probe2

Name of the second channel used for the probe or the custom name assigned to the channel in the index file. eg. "FSC.A", "FSC.H", "SSC.A","DsRed.A", "PE.Cy5_5.A", "PE.Cy7.A","BV650.A", "BV711.A","Alexa.Fluor.700.A" "APC.Cy7.A","PerCP.Cy5.5.A","Time"

posvalue_probe1

Threshold used for fluorescence intensities to be considered as positive for the first probe

posvalue_probe2

Threshold used for fluorescence intensities to be considered as positive for the second probe

cdr3_start

Expected CDR3 starting position, that depends on your primer set. Default is position 100

cdr3_end

Expected CDR3 end position, that depends on your primer set. Default is position 150

Value

Saves HTML reports, fasta files, csv files

Examples

quality_report(
    folder_sequences = system.file("extdata/sorted_sangerseq",
        package = "scifer"),
    outputfile = "QC-report.html",
     # output to a temporary directory
    output_dir = tempdir(),
    folder_path_fcs = system.file("/extdata/fcs_index_sorting",
        package = "scifer"),
    processors = 1, compensation = TRUE, plate_wells = "96",
    probe1 = "Pre.F", probe2 = "Post.F",
    posvalue_probe1 = 600, posvalue_probe2 = 400,
    cdr3_start = 100,
    cdr3_end = 150
)


rodrigarc/RepertoiR documentation built on Aug. 14, 2024, 6:29 a.m.