Extract All Fragments
extract_fragments.RdExtracts peak data from each sample in a list of fragments.
Examples
gm_raw <- trace::example_data
metadata <- trace::metadata
test_fragments <- peak_table_to_fragments(gm_raw,
data_format = "genemapper5",
dye_channel = "B",
min_size_bp = 400
)
add_metadata(
fragments_list = test_fragments,
metadata_data.frame = metadata
)
find_alleles(
fragments_list = test_fragments
)
call_repeats(
fragments_list = test_fragments,
assay_size_without_repeat = 87,
repeat_size = 3
)
extract_alleles(test_fragments)
#> unique_id allele_size allele_signal
#> 20230413_A07.fsa 20230413_A07.fsa 480.54 1240
#> 20230413_A08.fsa 20230413_A08.fsa 480.54 1230
#> 20230413_A09.fsa 20230413_A09.fsa 486.32 1284
#> 20230413_C01.fsa 20230413_C01.fsa 482.43 1068
#> 20230413_C02.fsa 20230413_C02.fsa 480.10 1164
#> 20230413_C03.fsa 20230413_C03.fsa 480.30 1083
#> 20230413_D07.fsa 20230413_D07.fsa 478.16 1361
#> 20230413_D08.fsa 20230413_D08.fsa 475.33 1382
#> 20230413_D09.fsa 20230413_D09.fsa 475.37 1123
#> 20230413_F01.fsa 20230413_F01.fsa 476.53 807
#> 20230413_F02.fsa 20230413_F02.fsa 474.28 1001
#> 20230413_F03.fsa 20230413_F03.fsa 477.33 948
#> 20230413_G07.fsa 20230413_G07.fsa 466.33 3363
#> 20230413_G08.fsa 20230413_G08.fsa 466.67 1918
#> 20230413_G09.fsa 20230413_G09.fsa 466.32 3935
#> 20230413_H07.fsa 20230413_H07.fsa 414.55 3798
#> 20230413_H08.fsa 20230413_H08.fsa 420.70 2081
#> S-21-211_20220630.fsa S-21-211_20220630.fsa 412.74 1944
#> S-21-212_20220630.fsa S-21-212_20220630.fsa 418.75 1902
#> allele_repeat allele_2_size allele_2_signal
#> 20230413_A07.fsa 131.1800 NA NA
#> 20230413_A08.fsa 131.1800 NA NA
#> 20230413_A09.fsa 133.1067 NA NA
#> 20230413_C01.fsa 131.8100 NA NA
#> 20230413_C02.fsa 131.0333 NA NA
#> 20230413_C03.fsa 131.1000 NA NA
#> 20230413_D07.fsa 130.3867 NA NA
#> 20230413_D08.fsa 129.4433 NA NA
#> 20230413_D09.fsa 129.4567 NA NA
#> 20230413_F01.fsa 129.8433 NA NA
#> 20230413_F02.fsa 129.0933 NA NA
#> 20230413_F03.fsa 130.1100 NA NA
#> 20230413_G07.fsa 126.4433 NA NA
#> 20230413_G08.fsa 126.5567 NA NA
#> 20230413_G09.fsa 126.4400 NA NA
#> 20230413_H07.fsa 109.1833 NA NA
#> 20230413_H08.fsa 111.2333 NA NA
#> S-21-211_20220630.fsa 108.5800 NA NA
#> S-21-212_20220630.fsa 110.5833 NA NA
#> allele_2_repeat
#> 20230413_A07.fsa NA
#> 20230413_A08.fsa NA
#> 20230413_A09.fsa NA
#> 20230413_C01.fsa NA
#> 20230413_C02.fsa NA
#> 20230413_C03.fsa NA
#> 20230413_D07.fsa NA
#> 20230413_D08.fsa NA
#> 20230413_D09.fsa NA
#> 20230413_F01.fsa NA
#> 20230413_F02.fsa NA
#> 20230413_F03.fsa NA
#> 20230413_G07.fsa NA
#> 20230413_G08.fsa NA
#> 20230413_G09.fsa NA
#> 20230413_H07.fsa NA
#> 20230413_H08.fsa NA
#> S-21-211_20220630.fsa NA
#> S-21-212_20220630.fsa NA