quality_report: Generate general and individualized reports

In rodrigarc/RepertoiR: Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

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.