Description Usage Arguments Value Examples
This function can deal with both multifast5 files and single fast5 files. It can handle files basecalled with standard or the flip flop model.
1 2 3 | extract_read_data(file_path = NA, read_id_fast5_file = NA,
plot_debug = FALSE, basecalled_with, basecall_group, multifast5, model,
plotting_library)
|
file_path |
a character string [NA]. Path of the single fast5 file. Use it if the file to be read is a single fast file. If the file to be read is multifast5 file, then keep this parameter as NA. Also set multifast5 flag to FALSE |
read_id_fast5_file |
a list [NA]. A list of 'read_id' and 'fast5_file' path. Use this option when a read from a multifast5 file is to be read. In such a case, you should set file_path to NA, and set multifast5 flag to TRUE. |
plot_debug |
a logical [FALSE]. Should data for plotting debug info in the plots be computed |
basecalled_with |
a character string. Specify if the data is from 'albacore' or 'guppy' |
basecall_group |
a character string. Name of the level in the Fast5 file hierarchy from which to read the data e.g. "Basecall_1D_000" |
multifast5 |
a logical. Set it to TRUE if the file to be processed is multifast5. Set it to FALSE if the file to be processed is a single fast5 file |
model |
a string. Set to 'flipflop' if the basecalling model is flipflop. Set to 'standard' if the basecalling model is standard model. |
plotting_library |
a string |
a list
1 2 3 4 5 6 7 8 9 10 11 12 | ## Not run:
extract_read_data(file_path = '/path/to/the/file',
read_id_fast5_file = NA,
plot_debug = F,
basecalled_with = 'albacore',
basecall_group = 'Basecall_1D_000',
multifast5 = TRUE,
model = 'standard',
plotting_library = 'rbokeh')
## End(Not run)
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