secondary_peaks: Check for secondary peaks in a sangerseq object

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

Check for secondary peaks in a sangerseq object

Description

This function finds and reports secondary peaks in a sangerseq object. It returns a table of secondary peaks, and optionally saves an annotated chromatogram and a csv file of the peak locations.

Usage

secondary_peaks(
  s,
  ratio = 0.33,
  output.folder = NA,
  file.prefix = "seq",
  processors = NULL
)

Arguments

s	a sangerseq s4 object from the sangerseqR package
ratio	Ratio of the height of a secondary peak to a primary peak. Secondary peaks higher than this ratio are annotated. Those below the ratio are not.
output.folder	If output.folder is NA (the default) no files are written. If a valid folder is provided, two files are written to that folder: a .csv file of the secondary peaks (see description below) and a .pdf file of the chromatogram.
file.prefix	If output.folder is specified, this is the prefix which will be appended to the .csv and the .pdf file. The default is "seq".
processors	Number of processors to use, or NULL (the default) for all available processors

Value

A list with two elements:

1. secondary.peaks: a data frame with one row per secondary peak above the ratio, and three columns: "position" is the position of the secondary peak relative to the primary sequence; "primary.basecall" is the primary base call; "secondary.basecall" is the secondary basecall.
   

2. read: the input sangerseq s4 object after having the makeBaseCalls() function from sangerseqR applied to it. This re-calls the primary and secondary bases in the sequence, and resets a lot of the internal data.

Examples

## Read abif using sangerseqR package
s4_sangerseq <- sangerseqR::readsangerseq(
    system.file("/extdata/sorted_sangerseq/E18_C1/A1_3_IgG_Inner.ab1",
        package = "scifer"
    )
)

## Summarise using summarise_abi_file()
processed_seq <- scifer:::secondary_peaks(s4_sangerseq)

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