scf-class {sangerseqR} | R Documentation

## Scf Class Objects

### Description

S4 object returned by `read.scf` containing all fields in the SCF file format (see http://staden.sourceforge.net/manual/formats_unix_2.html). Must be converted to `sangerseq` to be used in other functions from this package.

### Slots

`header`

  Header information from the file.

`sample_points`

  Trace data matrix (Order = A, C, G, T).

`sequence_probs`

  Matrix of the relative probabilities for each base at each position (Order = A, C, G, T).

`basecall_positions`

  Vector containing trace matrix indices for each basecall.

`basecalls`

  `DNAString` object containing the basecalls.

`comments`

  String containing any comments in the file.

`private`

  Raw binary data containing any private data in the file. Generally not used.

### See Also

`read.scf`, `abif`, `sangerseq`

### Examples

    homoscf <- read.scf(system.file("extdata",
                                    "homozygous.scf",
                                    package = "sangerseqR"))
    str(homoscf)

[Package sangerseqR version 1.18.0 Index]