Return subsets of a metabarlist object which meet user-defined conditions.
subset_metabarlist(metabarlist, table, indices)a metabarlist object
the table where the information on which the subsetting is based. Can be one of `reads`, `motus`, `pcrs`, or `samples`.
a boolean vector indicating the elements,
i.e. rows or columns to keep.
Elements to keep should be encoded TRUE.
a metabarlist object similar to the initial `metabarlist` except that it contains only the selected elements.
Subsetting a metabarlist will select specific rows from the `reads`, `motus`, `pcrs`, or `samples` tables. Factor levels that are unused after selection are dropped. Note however that:
If the selection is done on `reads`, `pcrs` or `samples`, the MOTUs not occurring in the pcrs or samples selected (i.e. those having a total number of reads of 0) are dropped.
If the selection is done on `motus`, the pcrs and samples where none of the selected MOTUs are found are kept.
data(soil_euk)
## Create a subset of soil_euk containing only annelid MOTUs
# i.e. by searching for "Annelida" in MOTUs taxonomic assignments
annelids <- subset_metabarlist(soil_euk,
table = "motus",
indices = grepl("Annelida", soil_euk$motus$path))
#> Warning: Some PCRs in out have a number of reads of zero in table `reads`!
summary_metabarlist(annelids)
#> $dataset_dimension
#> n_row n_col
#> reads 384 338
#> motus 338 15
#> pcrs 384 11
#> samples 64 8
#>
#> $dataset_statistics
#> nb_reads nb_motus avg_reads sd_reads avg_motus sd_motus
#> pcrs 247553 338 644.6693 909.0428 10.69271 9.802453
#> samples 247346 338 966.1953 964.2296 15.95703 7.782466
#>
## Create a subset of soil_euk containing only pcrs conducted in plate 1
plate1 <- subset_metabarlist(soil_euk,
table = "pcrs",
indices = (soil_euk$pcrs$plate_no == 1))
#> Warning: Some PCRs in out have a number of reads of zero in table `reads`!
summary_metabarlist(plate1)
#> $dataset_dimension
#> n_row n_col
#> reads 96 7900
#> motus 7900 15
#> pcrs 96 11
#> samples 64 8
#>
#> $dataset_statistics
#> nb_reads nb_motus avg_reads sd_reads avg_motus sd_motus
#> pcrs 1019783 7900 10622.74 11545.62 336.7917 278.5738
#> samples 771321 7730 12051.89 10578.45 495.0938 200.8483
#>
## Create a subset of soil_euk containing only positive controls
# i.e. excluding biological samples too that are NA in soil_euk$pcrs$control_type
poscontrols <- subset_metabarlist(soil_euk,
table = "pcrs",
indices = (soil_euk$pcrs$control_type == "positive" &
!is.na(soil_euk$pcrs$control_type)))
#> Warning: None of the selected elements are described in the initial samples table;
#> an empty sample data.frame is returned
summary_metabarlist(poscontrols)
#> $dataset_dimension
#> n_row n_col
#> reads 32 484
#> motus 484 15
#> pcrs 32 11
#> samples 8 0
#>
#> $dataset_statistics
#> nb_reads nb_motus avg_reads sd_reads avg_motus sd_motus
#> pcrs 342205 484 10693.91 9250.06 55.375 24.44711
#> samples 0 0 NaN NA NaN NA
#>