Summarize the sequences data, custom reports, and scrapped data in a strollur object
Source:R/summary.R
summary.RdSummarize the sequences data, custom reports, and scrapped data in a strollur object
Arguments
- data,
a strollur object
- type,
string containing the type of data you want the number of. Options include: "sequence", "report" and "scrap". Default = "sequence".
- report_type,
string containing the report type you would summarized. For example, the miseq_sop_example includes contigs assembly data and can be accessed with report_type = "contigs_report". Default = NULL.
- verbose,
boolean indicating whether or not you want progress messages. Default = TRUE.
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 summary of your FASTA data
summary(data = miseq, type = "sequence")
#> starts ends nbases ambigs polymers numns numseqs
#> Minimum: 1 375 249.0000 0 3.000000 0 1.000
#> 2.5%-tile: 1 375 252.0000 0 4.000000 0 2849.075
#> 25%-tile: 1 375 252.0000 0 4.000000 0 28490.750
#> Median: 1 375 253.0000 0 4.000000 0 56981.500
#> 75%-tile: 1 375 253.0000 0 5.000000 0 85472.250
#> 97.5%-tile: 1 375 254.0000 0 6.000000 0 111113.925
#> Maximum: 1 375 256.0000 0 6.000000 0 113963.000
#> Mean: 1 375 252.7406 0 4.496082 0 56981.643
#> starts ends nbases ambigs polymers numns numseqs
#> Minimum: 1 375 249.0000 0 3.000000 0 1.000
#> 2.5%-tile: 1 375 252.0000 0 4.000000 0 2849.075
#> 25%-tile: 1 375 252.0000 0 4.000000 0 28490.750
#> Median: 1 375 253.0000 0 4.000000 0 56981.500
#> 75%-tile: 1 375 253.0000 0 5.000000 0 85472.250
#> 97.5%-tile: 1 375 254.0000 0 6.000000 0 111113.925
#> Maximum: 1 375 256.0000 0 6.000000 0 113963.000
#> Mean: 1 375 252.7406 0 4.496082 0 56981.643
# summarize contigs_report
summary(data = miseq, type = "report", report_type = "contigs_report")
#> Length Overlap_Length Overlap_Start Overlap_End MisMatches Num_Ns
#> Minimum: 250.0000 232.0000 0.000000 248.0000 0.000000 0
#> 2.5%-tile: 252.0000 246.0000 1.000000 250.0000 0.000000 0
#> 25%-tile: 252.0000 249.0000 2.000000 251.0000 0.000000 0
#> Median: 253.0000 249.0000 2.000000 251.0000 1.000000 0
#> 75%-tile: 253.0000 250.0000 2.000000 251.0000 5.000000 0
#> 97.5%-tile: 254.0000 251.0000 4.000000 253.0000 26.000000 0
#> Maximum: 270.0000 255.0000 22.000000 256.0000 120.000000 0
#> Mean: 252.7575 249.1501 2.005361 251.1555 5.162474 0
#> Expected_Errors
#> Minimum: 1.00000000
#> 2.5%-tile: 1.00000000
#> 25%-tile: 1.00000000
#> Median: 1.00000000
#> 75%-tile: 1.00000000
#> 97.5%-tile: 1.00000000
#> Maximum: 4.00000000
#> Mean: 0.07385095
#> Length Overlap_Length Overlap_Start Overlap_End MisMatches Num_Ns
#> Minimum: 250.0000 232.0000 0.000000 248.0000 0.000000 0
#> 2.5%-tile: 252.0000 246.0000 1.000000 250.0000 0.000000 0
#> 25%-tile: 252.0000 249.0000 2.000000 251.0000 0.000000 0
#> Median: 253.0000 249.0000 2.000000 251.0000 1.000000 0
#> 75%-tile: 253.0000 250.0000 2.000000 251.0000 5.000000 0
#> 97.5%-tile: 254.0000 251.0000 4.000000 253.0000 26.000000 0
#> Maximum: 270.0000 255.0000 22.000000 256.0000 120.000000 0
#> Mean: 252.7575 249.1501 2.005361 251.1555 5.162474 0
#> Expected_Errors
#> Minimum: 1.00000000
#> 2.5%-tile: 1.00000000
#> 25%-tile: 1.00000000
#> Median: 1.00000000
#> 75%-tile: 1.00000000
#> 97.5%-tile: 1.00000000
#> Maximum: 4.00000000
#> Mean: 0.07385095
# remove sample 'F3D0' to produce a scrap report
xdev_remove_samples(data = miseq, samples = c("F3D0"))
#> miseq_sop:
#>
#> starts ends nbases ambigs polymers numns numseqs
#> Minimum: 1 375 249 0 3 0 1.00
#> 2.5%-tile: 1 375 252 0 4 0 2694.30
#> 25%-tile: 1 375 252 0 4 0 26943.00
#> Median: 1 375 253 0 4 0 53886.00
#> 75%-tile: 1 375 253 0 5 0 80829.00
#> 97.5%-tile: 1 375 254 0 6 0 105077.70
#> Maximum: 1 375 256 0 6 0 107772.00
#> Mean: 1 375 252 0 4 0 53886.14
#>
#> scrap_summary:
#> type trash_code unique total
#> 1 sequence remove_samples 101 109
#> 2 otu remove_samples 14 14
#> 3 asv remove_samples 101 109
#> 4 phylotype remove_samples 2 2
#>
#> Number of unique seqs: 2324
#> Total number of seqs: 107772
#>
#> Total number of samples: 18
#> Total number of treatments: 2
#> Total number of otus: 517
#> Total number of otu bin classifications: 517
#> Total number of asvs: 2324
#> Total number of asv bin classifications: 2324
#> Total number of phylotypes: 61
#> Total number of phylotype bin classifications: 61
#> Total number of sequence classifications: 2324
#> Total number of resource references: 2
#> Total number of custom reports: 1
#> Your dataset includes metadata
#>
# summarize FASTA data after removal of sample F3D0
summary(data = miseq, type = "sequence")
#> starts ends nbases ambigs polymers numns numseqs
#> Minimum: 1 375 249.0000 0 3.000000 0 1.00
#> 2.5%-tile: 1 375 252.0000 0 4.000000 0 2694.30
#> 25%-tile: 1 375 252.0000 0 4.000000 0 26943.00
#> Median: 1 375 253.0000 0 4.000000 0 53886.00
#> 75%-tile: 1 375 253.0000 0 5.000000 0 80829.00
#> 97.5%-tile: 1 375 254.0000 0 6.000000 0 105077.70
#> Maximum: 1 375 256.0000 0 6.000000 0 107772.00
#> Mean: 1 375 252.7345 0 4.493546 0 53886.14
#> starts ends nbases ambigs polymers numns numseqs
#> Minimum: 1 375 249.0000 0 3.000000 0 1.00
#> 2.5%-tile: 1 375 252.0000 0 4.000000 0 2694.30
#> 25%-tile: 1 375 252.0000 0 4.000000 0 26943.00
#> Median: 1 375 253.0000 0 4.000000 0 53886.00
#> 75%-tile: 1 375 253.0000 0 5.000000 0 80829.00
#> 97.5%-tile: 1 375 254.0000 0 6.000000 0 105077.70
#> Maximum: 1 375 256.0000 0 6.000000 0 107772.00
#> Mean: 1 375 252.7345 0 4.493546 0 53886.14
# summarize scrapped data -
# sequences and bins scrapped by removing the sample "F3D0"
summary(data = miseq, type = "scrap")
#> type trash_code unique total
#> 1 sequence remove_samples 101 109
#> 2 otu remove_samples 14 14
#> 3 asv remove_samples 101 109
#> 4 phylotype remove_samples 2 2
#> type trash_code unique total
#> 1 sequence remove_samples 101 109
#> 2 otu remove_samples 14 14
#> 3 asv remove_samples 101 109
#> 4 phylotype remove_samples 2 2