Returns reads for which the second-smallest finite distance is within
margin of the smallest distance. In hierarchical results, distances to
bins outside the read's parent abundance bin are NA and are ignored.
Reads with fewer than two finite distances are omitted. The margin is an
absolute difference on the algorithm's distance scale, not a probability.
Arguments
- x
A MetabinResult object.
- margin
Nonnegative maximum difference between the two smallest distances. Defaults to
0.05.
Value
A S4Vectors::DataFrame with read_id, bin, best_distance,
second_distance, and distance_margin, in input order.
Examples
res <- composition_based_binning(
system.file("extdata", "reads.metagenome.fasta.gz", package = "metabinR"),
dryRun = TRUE, kMerSizeCB = 2, numOfClustersCB = 2
)
ambiguous_reads(res, margin = 0.05)
#> DataFrame with 142 rows and 5 columns
#> read_id bin best_distance second_distance distance_margin
#> <character> <character> <numeric> <numeric> <numeric>
#> 1 S0R235/1 1 60 60 0
#> 2 S0R350/1 1 78 78 0
#> 3 S0R451/2 1 60 60 0
#> 4 S0R623/1 1 68 68 0
#> 5 S0R747/1 1 76 76 0
#> ... ... ... ... ... ...
#> 138 S0R12993/2 1 60 60 0
#> 139 S0R12996/1 1 60 60 0
#> 140 S0R13037/2 1 64 64 0
#> 141 S0R13043/1 1 68 68 0
#> 142 S0R13268/2 1 62 62 0