summarise_quality: Summary table of quality measurements from Sanger sequencing

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

Summary table of quality measurements from Sanger sequencing

Description

Generate a summary table containing quality measurements from Sanger sequencing '.abi' files. This function will read all the '.abi' files in a folder, and generate a summary table containing basic quality metrics.

Usage

summarise_quality(
  folder_sequences = "input_folder",
  trim.cutoff = 0.01,
  secondary.peak.ratio = 0.33,
  processors = NULL
)

Arguments

folder_sequences	Folder containing all the sanger sequencing abi/ab1 files on subfolders. Each subfolder should have have a identifiable name, matching name with fcs data. eg. "E18_01", "E23_06". The first characters of the ab1 file name should be the well location. eg. "A1-sequence1.ab1", "F8_sequence-igg.ab1"
trim.cutoff	Cutoff at which you consider a base to be bad. This works on a logarithmic scale, such that if you want to consider a score of 10 as bad, you set cutoff to 0.1; for 20 set it at 0.01; for 30 set it at 0.001; for 40 set it at 0.0001; and so on. Contiguous runs of bases below this quality will be removed from the start and end of the sequence. Given the high quality reads expected of most modern ABI sequencers, the defualt is 0.0001.
secondary.peak.ratio	Ratio of the height of a secondary peak to a primary peak. Secondary peaks higher than this ratio are annotated, while those below the ratio are not.
processors	Number of processors to use, or NULL (the default) for all available processors

Value

List containing two items: * summaries: contains all the summary results from the processed abi files, * quality_scores: contains all the Phred quality score for each position.

Examples

sf <- summarise_quality(
    folder_sequences = system.file("extdata/sorted_sangerseq",
        package = "scifer"
    ),
    secondary.peak.ratio = 0.33,
    trim.cutoff = 0.01,
    processor = 1
)

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