peak_table_to_fragments | R Documentation |
This function converts a peak table data frame into a list of fragments_repeats objects.
peak_table_to_fragments(
df,
data_format = NULL,
peak_size_col = NULL,
peak_signal_col = NULL,
unique_id = NULL,
dye_col = NULL,
dye_channel = NULL,
allele_col = NULL,
min_size_bp = 200,
max_size_bp = 1000
)
df |
A data frame containing the peak data. |
data_format |
The format that the data frame is in (for example, a genemapper peak table). Choose between: genemapper5, generic. |
peak_size_col |
A character string specifying column name giving the peak size. |
peak_signal_col |
A character string specifying column name giving the peak signal. |
unique_id |
A character string specifying column name giving the unique sample id (often the file name). |
dye_col |
Genemapper specific. A character string specifying column name indicating the dye channel. |
dye_channel |
Genemapper specific. A character string indicating the channel to extract data from. For example, 6-FAM is often "B". |
allele_col |
Genemapper specific. A character string specifying column name indicating the called alleles. This is often used when the peaks have been called in genemapper. |
min_size_bp |
Numeric value indicating the minimum size of the peak table to import. |
max_size_bp |
Numeric value indicating the maximum size of the peak table to import. |
This function takes a peak table data frame (eg. Genemapper output) and converts it into a list of fragment objects. The function supports different data formats and allows specifying column names for various attributes.
A list of fragments_repeats objects.
repeat_table_to_repeats
gm_raw <- trace::example_data
test_fragments <- peak_table_to_fragments(
gm_raw,
data_format = "genemapper5",
dye_channel = "B",
min_size_bp = 400
)
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