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: "sequences", "reports" and "scrap". Default = "sequences".
- 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 = "sequences")
#> 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 3.000000 0 2850.075
#> 25%-tile: 1 375 252.0000 0 4.000000 0 28491.750
#> Median: 1 375 252.0000 0 4.000000 0 56982.500
#> 75%-tile: 1 375 253.0000 0 5.000000 0 85473.250
#> 97.5%-tile: 1 375 253.0000 0 6.000000 0 111114.925
#> Maximum: 1 375 256.0000 0 6.000000 0 113963.000
#> Mean: 1 375 252.4472 0 4.368699 0 0.000
#> 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 3.000000 0 2850.075
#> 25%-tile: 1 375 252.0000 0 4.000000 0 28491.750
#> Median: 1 375 252.0000 0 4.000000 0 56982.500
#> 75%-tile: 1 375 253.0000 0 5.000000 0 85473.250
#> 97.5%-tile: 1 375 253.0000 0 6.000000 0 111114.925
#> Maximum: 1 375 256.0000 0 6.000000 0 113963.000
#> Mean: 1 375 252.4472 0 4.368699 0 0.000
# summarize contigs_report
summary(data = miseq, type = "reports", report_type = "contigs_report")
#> Expected_Errors Length MisMatches Num_Ns Overlap_End
#> Minimum: 0.0000452496 250.0000 0.000000 0 248.0000
#> 2.5%-tile: 0.0016101600 252.0000 0.000000 0 251.0000
#> 25%-tile: 0.0028177700 252.0000 0.000000 0 251.0000
#> Median: 0.0062948698 252.0000 2.000000 0 251.0000
#> 75%-tile: 0.0264780000 253.0000 4.000000 0 251.0000
#> 97.5%-tile: 1.1412299871 253.0000 76.000000 0 252.0000
#> Maximum: 3.0126200000 270.0000 120.000000 0 256.0000
#> Mean: 0.0984788569 252.5128 7.534147 0 251.0762
#> Overlap_Length Overlap_Start
#> Minimum: 232.0000 0.000000
#> 2.5%-tile: 248.0000 1.000000
#> 25%-tile: 249.0000 2.000000
#> Median: 249.0000 2.000000
#> 75%-tile: 249.0000 2.000000
#> 97.5%-tile: 251.0000 3.000000
#> Maximum: 255.0000 22.000000
#> Mean: 249.2136 1.862692
#> Expected_Errors Length MisMatches Num_Ns Overlap_End
#> Minimum: 0.0000452496 250.0000 0.000000 0 248.0000
#> 2.5%-tile: 0.0016101600 252.0000 0.000000 0 251.0000
#> 25%-tile: 0.0028177700 252.0000 0.000000 0 251.0000
#> Median: 0.0062948698 252.0000 2.000000 0 251.0000
#> 75%-tile: 0.0264780000 253.0000 4.000000 0 251.0000
#> 97.5%-tile: 1.1412299871 253.0000 76.000000 0 252.0000
#> Maximum: 3.0126200000 270.0000 120.000000 0 256.0000
#> Mean: 0.0984788569 252.5128 7.534147 0 251.0762
#> Overlap_Length Overlap_Start
#> Minimum: 232.0000 0.000000
#> 2.5%-tile: 248.0000 1.000000
#> 25%-tile: 249.0000 2.000000
#> Median: 249.0000 2.000000
#> 75%-tile: 249.0000 2.000000
#> 97.5%-tile: 251.0000 3.000000
#> Maximum: 255.0000 22.000000
#> Mean: 249.2136 1.862692
# remove sample 'F3D0' to produce a scrap report
xdev_remove_samples(data = miseq, samples = c("F3D0"))
# summarize FASTA data after removal of sample F3D0
summary(data = miseq, type = "sequences")
#> starts ends nbases ambigs polymers numns numseqs
#> Minimum: 1 375 249.0000 0 3.000000 0 1.0
#> 2.5%-tile: 1 375 252.0000 0 3.000000 0 2695.3
#> 25%-tile: 1 375 252.0000 0 4.000000 0 26944.0
#> Median: 1 375 252.0000 0 4.000000 0 53887.0
#> 75%-tile: 1 375 253.0000 0 5.000000 0 80830.0
#> 97.5%-tile: 1 375 253.0000 0 6.000000 0 105078.7
#> Maximum: 1 375 256.0000 0 6.000000 0 107772.0
#> Mean: 1 375 252.4444 0 4.361532 0 0.0
#> starts ends nbases ambigs polymers numns numseqs
#> Minimum: 1 375 249.0000 0 3.000000 0 1.0
#> 2.5%-tile: 1 375 252.0000 0 3.000000 0 2695.3
#> 25%-tile: 1 375 252.0000 0 4.000000 0 26944.0
#> Median: 1 375 252.0000 0 4.000000 0 53887.0
#> 75%-tile: 1 375 253.0000 0 5.000000 0 80830.0
#> 97.5%-tile: 1 375 253.0000 0 6.000000 0 105078.7
#> Maximum: 1 375 256.0000 0 6.000000 0 107772.0
#> Mean: 1 375 252.4444 0 4.361532 0 0.0
# 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