Generate a table representing the frequency of unique mutations. In order to ensure confidence in the results, a threshold is provided indicating confidence in genotype calls. All data that do not meet this threshold will be removed from the computation.
Arguments
- data
A data frame, data frame extension (e.g. a tibble), or a lazy data frame (e.g. from dbplyr or dtplyr).
- threshold
A minimum UMI count which reflects the confidence in the genotype call. Data with a UMI count of less than the threshold will be filtered out from the analysis.
Value
A tibble with the extra class mut_freq. The
output has the following columns:
mutation_name: The unique mutation sequenced.frequency: The frequency of the mutation.
See also
plot_mutation_frequency() for plotting the table.
Examples
ref_file <- miplicorn_example("reference_AA_table.csv")
alt_file <- miplicorn_example("alternate_AA_table.csv")
cov_file <- miplicorn_example("coverage_AA_table.csv")
data <- read_tbl_ref_alt_cov(
ref_file,
alt_file,
cov_file,
gene == "atp6" | gene == "crt"
)
mutation_frequency(data, 5)
#> # A tibble: 16 × 2
#> mutation_name frequency
#> <chr> <dbl>
#> 1 atp6-Ala623Glu 0
#> 2 atp6-Glu431Lys 0
#> 3 atp6-Gly639Asp 0.183
#> 4 atp6-Ser466Asn 0.129
#> 5 atp6-Ser769Asn 0
#> 6 crt-Ala220Ser 0.128
#> 7 crt-Asn326Asp 0.101
#> 8 crt-Asn326Ser 0
#> 9 crt-Asn75Glu 0.0533
#> 10 crt-Cys72Ser 0.146
#> 11 crt-His97Leu 0
#> 12 crt-His97Tyr 0
#> 13 crt-Ile356Leu 0.130
#> 14 crt-Ile356Thr 0.0507
#> 15 crt-Lys76Thr 0.200
#> 16 crt-Met74Ile 0.0533