Find the number of sequences, samples, treatments or bins of a given type in a strollur object
Arguments
- data,
a strollur object
- type,
string containing the type of data you want the number of. Options include: "sequences", "samples", "treatments", "bins" and "references". Default = "sequences".
- bin_type,
string containing the bin type you would like the number of bins for. Default = "otu".
- samples,
vector of strings. samples is only used when 'type' = "sequences" or 'type' = "bins" . samples should contain the names of the samples you want the count for. Default = NULL.
- distinct,
Boolean. distinct is used when 'type' = "sequences" or 'type' = "bins". When 'type' = "sequences" and distinct is TRUE the number of unique sequences is returned. When 'type' = "sequences" and distinct is FALSE total number of sequences is returned. This can also be combined with samples to find the number of unique sequences found only in a given set of samples, or to find the total number of sequences in a given set of samples. When 'type' = "bins", you can set distinct = TRUE to return the number of bins that ONLY contain sequences from the given samples. When distinct is FALSE the count returned contains bins with sequences from a given samples, but those bins may also contain other samples. Default = FALSE.
Examples
miseq <- miseq_sop_example()
#> Added 2425 sequences.
#> Assigned 2425 sequence abundances.
#> Assigned 2425 sequence taxonomies.
#> Assigned 531 otu bins.
#> Assigned 2425 asv bins.
#> Assigned 63 phylotype bins.
#> Assigned 19 samples to treatments.
#> Assigned 531 otu bin taxonomies.
#> Assigned 531 otu bin representative sequences.
#> Added metadata.
#> Added 2 resource references.
#> Added a contigs_report.
# To get the total number of sequences
xdev_count(data = miseq, type = "sequences")
#> [1] 113963
# To get number of unique sequences
xdev_count(data = miseq, type = "sequences", distinct = TRUE)
#> [1] 2425
# To get number of unique sequences from samples 'F3D0' and 'F3D1'
# Note these sequences will be present in both samples but may be
# be present in other samples as well
xdev_count(data = miseq, type = "sequences", samples = c("F3D0", "F3D1"))
#> [1] 9385
# To get number of unique sequences exclusive to samples 'F3D0' and 'F3D1'
# Note these sequences are present in both samples and NOT present in
# other samples
xdev_count(data = miseq, type = "sequences", samples = c("F3D0", "F3D1"),
distinct = TRUE)
#> [1] 2
# To get the number of samples in the dataset
xdev_count(data = miseq, type = "samples")
#> [1] 19
# To get the number of treatments in the dataset
xdev_count(data = miseq, type = "treatments")
#> [1] 2
# To get the number of "otu" bins in the dataset
xdev_count(data = miseq, type = "bins", bin_type = "otu")
#> [1] 531
# To get the number of "asv" bins in the dataset
xdev_count(data = miseq, type = "bins", bin_type = "asv")
#> [1] 2425
# To get the number of "phylotype" bins in the dataset
xdev_count(data = miseq, type = "bins", bin_type = "phylotype")
#> [1] 63
# To get number of bins from samples 'F3D0' and 'F3D1'
# Note these bins will have sequences from both samples but there may be
# other samples present as well
xdev_count(data = miseq, type = "bins", samples = c("F3D0", "F3D1"))
#> [1] 125
# To get number of bins unique to samples 'F3D0' and 'F3D1'
# Note these bins will have sequences from both samples and NO other samples
# will be present in the bins.
xdev_count(data = miseq, type = "bins", samples = c("F3D0", "F3D1"),
distinct = TRUE)
#> [1] 1