fragments_trace {trace} | R Documentation |
fragments_trace object
Description
An R6 Class representing a fragments_trace object.
Details
The idea behind this class is to store data for processing of the continuous trace-level information from an fsa file towards peak level data.
It also contains methods for plotting the ladder and traces
Super class
trace::fragments
-> fragments_trace
Public fields
unique_id
unique id of the sample usually the file name
fsa
The whole fsa file, output from seqinr::read.abif()
raw_ladder
The raw data from the ladder channel
raw_data
The raw data from the sample channel
scan
The scan number
off_scale_scans
vector indicating which scales were too big and off scale. Note can be in any channel
ladder_df
A dataframe of the identified ladder from
find_ladders()
. Scan is the scan number of peak and size is the associated bp size.trace_bp_df
A dataframe of bp size for every scan from
find_ladders()
.
Methods
Public methods
Inherited methods
Method new()
Create a new fragments_trace.
Usage
fragments_trace$new(unique_id, fsa_file)
Arguments
unique_id
usually the file name
fsa_file
output from seqinr::read.abif()
Returns
A new fragments_trace
object.
Method plot_ladder()
plot the ladder data
Usage
fragments_trace$plot_ladder(xlim = NULL, ylim = NULL, plot_title = NULL)
Arguments
xlim
numeric vector length two specifying the x axis limits
ylim
numeric vector length two specifying the y axis limits
plot_title
A character string for setting the plot title. Defaults to the unique id of the object
Returns
A base R plot
Method plot_data_channels()
plot the raw data channels in the fsa file. It identifies every channel that has "DATA" in its name.
Usage
fragments_trace$plot_data_channels()
Returns
A base R plot
Method clone()
The objects of this class are cloneable with this method.
Usage
fragments_trace$clone(deep = FALSE)
Arguments
deep
Whether to make a deep clone.