scf-class: Scf Class Objects

In jonathonthill/sangerseqR: Tools for Sanger Sequencing Data in R

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)

jonathonthill/sangerseqR documentation built on July 1, 2023, 4:55 p.m.