Extract Modal Peaks
extract_alleles.RdExtracts modal peak information from each sample in a list of fragments.
Examples
gm_raw <- trace::example_data
test_fragments <- peak_table_to_fragments(gm_raw,
data_format = "genemapper5",
dye_channel = "B",
min_size_bp = 400
)
find_alleles(
fragments_list = test_fragments,
peak_region_size_gap_threshold = 6,
peak_region_signal_threshold_multiplier = 1
)
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 NA NA NA
#> 20230413_A08.fsa NA NA NA
#> 20230413_A09.fsa NA NA NA
#> 20230413_C01.fsa NA NA NA
#> 20230413_C02.fsa NA NA NA
#> 20230413_C03.fsa NA NA NA
#> 20230413_D07.fsa NA NA NA
#> 20230413_D08.fsa NA NA NA
#> 20230413_D09.fsa NA NA NA
#> 20230413_F01.fsa NA NA NA
#> 20230413_F02.fsa NA NA NA
#> 20230413_F03.fsa NA NA NA
#> 20230413_G07.fsa NA NA NA
#> 20230413_G08.fsa NA NA NA
#> 20230413_G09.fsa NA NA NA
#> 20230413_H07.fsa NA NA NA
#> 20230413_H08.fsa NA NA NA
#> S-21-211_20220630.fsa NA NA NA
#> S-21-212_20220630.fsa NA 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