Extract Modal Peaks
extract_alleles.RdExtracts modal peak information from each sample in a list of fragments.
Examples
fsa_list <- lapply(cell_line_fsa_list, function(x) x$clone())
# import data with read_fsa() to generate an equivalent list to cell_line_fsa_list
test_fragments <- trace(fsa_list, grouped = TRUE, metadata_data.frame = metadata)
#> Finding ladders
#>
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#> Finding fragments
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#> Finding alleles
#> Calling repeats
#> Assigning index peaks
extract_alleles(test_fragments)
#> unique_id allele_size allele_signal
#> 20230413_A07.fsa 20230413_A07.fsa 481.5436 1309
#> 20230413_A08.fsa 20230413_A08.fsa 481.5379 1307
#> 20230413_A09.fsa 20230413_A09.fsa 487.1819 1361
#> 20230413_C01.fsa 20230413_C01.fsa 483.4888 1161
#> 20230413_C02.fsa 20230413_C02.fsa 481.1637 1248
#> 20230413_C03.fsa 20230413_C03.fsa 481.3875 1157
#> 20230413_D07.fsa 20230413_D07.fsa 479.0952 1456
#> 20230413_D08.fsa 20230413_D08.fsa 476.3517 1465
#> 20230413_D09.fsa 20230413_D09.fsa 476.4824 1189
#> 20230413_F01.fsa 20230413_F01.fsa 477.6280 862
#> 20230413_F02.fsa 20230413_F02.fsa 475.3879 1056
#> 20230413_F03.fsa 20230413_F03.fsa 478.4716 1013
#> 20230413_G07.fsa 20230413_G07.fsa 467.2601 3585
#> 20230413_G08.fsa 20230413_G08.fsa 467.5702 2025
#> 20230413_G09.fsa 20230413_G09.fsa 467.3300 4201
#> 20230413_H07.fsa 20230413_H07.fsa 415.3404 3948
#> 20230413_H08.fsa 20230413_H08.fsa 421.3037 2152
#> S-21-211_20220630.fsa S-21-211_20220630.fsa 413.6654 2025
#> S-21-212_20220630.fsa S-21-212_20220630.fsa 419.4859 1996
#> allele_repeat allele_2_size allele_2_signal
#> 20230413_A07.fsa 131.5145 NA NA
#> 20230413_A08.fsa 131.5126 NA NA
#> 20230413_A09.fsa 133.3940 NA NA
#> 20230413_C01.fsa 132.1629 NA NA
#> 20230413_C02.fsa 131.3879 NA NA
#> 20230413_C03.fsa 131.4625 NA NA
#> 20230413_D07.fsa 130.6984 NA NA
#> 20230413_D08.fsa 129.7839 NA NA
#> 20230413_D09.fsa 129.8275 NA NA
#> 20230413_F01.fsa 130.2093 NA NA
#> 20230413_F02.fsa 129.4626 NA NA
#> 20230413_F03.fsa 130.4905 NA NA
#> 20230413_G07.fsa 126.7534 NA NA
#> 20230413_G08.fsa 126.8567 NA NA
#> 20230413_G09.fsa 126.7767 NA NA
#> 20230413_H07.fsa 109.4468 NA NA
#> 20230413_H08.fsa 111.4346 NA NA
#> S-21-211_20220630.fsa 108.8885 NA NA
#> S-21-212_20220630.fsa 110.8286 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