Get a data.frame containing the report. Reports include FASTA format, sequences reports, sequence_bin_assignments, sequence_taxonomy, bin_taxonomy, bin_representatives, sample_assignments, metadata, references, sequence_scrap, and bin_scrap in a strollur object.
Arguments
- data,
a strollur object
- type,
string containing the type of report you would like. Options include: "fasta", "sequences", "sequence_bin_assignments", "sequence_taxonomy", "bin_taxonomy", "bin_representatives", "sample_assignments", "metadata", "references", "sequence_scrap", "bin_scrap". If you have added custom reports for alignment, contigs_assembly or chimeras, you can get those as well. Default = "sequences".
- bin_type,
string containing the bin type you would like a bin_taxonomy report for. Default = "otu".
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 FASTA data
report(data = miseq, type = "fasta") |> head(n = 5)
#> sequence_names
#> 1 M00967_43_000000000-A3JHG_1_2101_16474_12783
#> 2 M00967_43_000000000-A3JHG_1_1113_12711_3318
#> 3 M00967_43_000000000-A3JHG_1_2108_14707_9807
#> 4 M00967_43_000000000-A3JHG_1_1110_4126_16552
#> 5 M00967_43_000000000-A3JHG_1_2102_8408_13436
#> sequences
#> 1 TAC--GG-AG-GAT--GCG-A-G-C-G-T-T--AT-C-CGTGAT--TT-A-T-T--GG-GT--TT-A-AA-GG-GT-GC-G-TA-GGC-G-G-A-CA-G-T-T-AA-G-T-C-A-G-C-G-G--TA-A-AA-TT-G-A-GA-GG--CT-C-AA-C-C-T-C-T-T-C--CC-G-C-CGTT-GAAAC-TG-A-TTGTC-TTGA-GT-GG-GC-GA-G-A---AG-T-A-TGTGGAATGCGTGGTGT-AGCGGT-GAAATGCATAG-AT-A-TC-AC-GC-AG-AACTCCGAT-TGCGAAGGCA------GCATA-CCG-G-CG-CC-C-A-ACTGACG-CTGA-AGCA-CGAAA-GCG-TGGGT-ATC-GAACAGG
#> 2 TAC--GT-AG-GGG--GCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GA-GC-G-TA-GGC-G-G-C-CA-T-G-C-AA-G-T-C-A-G-A-A-G--TG-A-AA-AC-C-C-GG-GG--CT-C-AA-C---C-C-TGG-G-AGT-G-C-TTTT-GAAAC-TG-T-GCGGC-TAGA-GT-GT-CG-GA-G-G---GG-T-A-AGTGGAATTCCTAGTGT-AGCGGT-GAAATGCGTAG-AT-A-TT-AG-GA-GG-AACACCAGT-GGCGAAGGCG------GCTTA-CTG-G-AC-GA-T-G-ACTGACG-CTGA-GGCT-CGAAA-GCG-TGGGT-ATC-GAACAGG
#> 3 TAC--GG-AG-GAT--GCG-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GA-GC-G-TA-GAC-G-G-C-GG-C-G-C-AA-G-T-C-T-G-A-A-G--TG-A-AA-GC-C-C-GT-GG--CT-C-AA-C-C-G-C-G-G-A-ACC-G-C-TTTG-GAAAC-TG-C-GAGGC-TGGA-GT-GC-TG-GA-G-A---GG-T-A-AGCGGAATTCCTGGTGT-AGCGGT-GAAATGCGTAG-AT-A-TC-AG-GA-GG-AACACCGGT-GGCGAAGGCG------GCTTA-CTG-G-AC-AG-T-G-ACTGACG-TTGA-GGCT-CGAAA-GCG-TGGGG-AGC-GAACAGG
#> 4 TAC--GG-AG-GAT--TCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-T-T--GG-GT--TT-A-AA-GG-GT-GC-G-TA-GGC-G-G-G-CT-G-T-T-AA-G-T-C-A-G-C-G-G--TC-A-AA-TG-T-C-GG-GG--CT-C-AA-C-C-C-C-G-G-C--CT-G-C-CGTT-GAAAC-TG-G-CGGCC-TCGA-GT-GG-GC-GA-G-A---AG-T-A-TGCGGAATGCGTGGTGT-AGCGGT-GAAATGCATAG-AT-A-TC-AC-GC-AG-AACTCCGAT-TGCGAAGGCA------GCATA-CCG-G-CG-CC-C-T-ACTGACG-CTGA-GGCA-CGAAA-GCG-TGGGT-ATC-GAACAGG
#> 5 TAC--GG-AG-GGG--GCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GA-GC-G-TA-GGC-G-G-C-AG-T-G-C-AA-G-T-C-A-G-A-A-G--TG-A-AA-GC-C-C-AA-GG--CT-C-AA-C---C-A-TGG-G-ACT-G-C-TTTT-GAAAC-TG-T-ACAGC-TAGA-TT-GC-AG-GA-G-A---GG-T-A-AGTGGAATTCCTAGTGT-AGCGGT-GAAATGCGTAG-AT-A-TT-AG-GA-GG-AACACCAGT-GGCGAAGGCG------GCTTA-CTG-G-AC-TG-T-A-AATGACG-CTGA-GGCT-CGAAA-GCG-TGGGG-AGC-AAACAGG
# To get a report about the FASTA data
report(data = miseq, type = "sequences") |> head(n = 5)
#> id start end length ambig
#> 1 M00967_43_000000000-A3JHG_1_2101_16474_12783 1 375 253 0
#> 2 M00967_43_000000000-A3JHG_1_1113_12711_3318 1 375 253 0
#> 3 M00967_43_000000000-A3JHG_1_2108_14707_9807 1 375 253 0
#> 4 M00967_43_000000000-A3JHG_1_1110_4126_16552 1 375 252 0
#> 5 M00967_43_000000000-A3JHG_1_2102_8408_13436 1 375 253 0
#> longest_homopolymer num_n
#> 1 4 0
#> 2 5 0
#> 3 4 0
#> 4 4 0
#> 5 5 0
# To get the sequence bin assignments
report(data = miseq, type = "sequence_bin_assignments", bin_type = "otu") |>
head(n = 5)
#> otu_id seq_id
#> 1 Otu001 M00967_43_000000000-A3JHG_1_1111_20933_6700
#> 2 Otu001 M00967_43_000000000-A3JHG_1_1113_17095_9759
#> 3 Otu001 M00967_43_000000000-A3JHG_1_1114_22144_24942
#> 4 Otu001 M00967_43_000000000-A3JHG_1_1112_5981_8948
#> 5 Otu001 M00967_43_000000000-A3JHG_1_2106_5509_18056
# To get the sample treatment assignments
report(data = miseq, type = "sample_assignments")
#> samples treatments
#> 1 F3D0 Early
#> 2 F3D1 Early
#> 3 F3D141 Late
#> 4 F3D142 Late
#> 5 F3D143 Late
#> 6 F3D144 Late
#> 7 F3D145 Late
#> 8 F3D146 Late
#> 9 F3D147 Late
#> 10 F3D148 Late
#> 11 F3D149 Late
#> 12 F3D150 Late
#> 13 F3D2 Early
#> 14 F3D3 Early
#> 15 F3D5 Early
#> 16 F3D6 Early
#> 17 F3D7 Early
#> 18 F3D8 Early
#> 19 F3D9 Early
# To get a report about sequence classifications
report(data = miseq, type = "sequence_taxonomy") |> head(n = 10)
#> sequence_names levels
#> 1 M00967_43_000000000-A3JHG_1_2101_16474_12783 1
#> 2 M00967_43_000000000-A3JHG_1_2101_16474_12783 2
#> 3 M00967_43_000000000-A3JHG_1_2101_16474_12783 3
#> 4 M00967_43_000000000-A3JHG_1_2101_16474_12783 4
#> 5 M00967_43_000000000-A3JHG_1_2101_16474_12783 5
#> 6 M00967_43_000000000-A3JHG_1_2101_16474_12783 6
#> 7 M00967_43_000000000-A3JHG_1_1113_12711_3318 1
#> 8 M00967_43_000000000-A3JHG_1_1113_12711_3318 2
#> 9 M00967_43_000000000-A3JHG_1_1113_12711_3318 3
#> 10 M00967_43_000000000-A3JHG_1_1113_12711_3318 4
#> taxonomies confidences
#> 1 Bacteria 100
#> 2 "Bacteroidetes" 100
#> 3 "Bacteroidia" 99
#> 4 "Bacteroidales" 99
#> 5 "Porphyromonadaceae" 88
#> 6 "Porphyromonadaceae"_unclassified 88
#> 7 Bacteria 100
#> 8 Firmicutes 100
#> 9 Clostridia 100
#> 10 Clostridiales 100
# To get a report about bin classifications for 'otu' data
report(data = miseq, type = "bin_taxonomy", bin_type = "otu") |> head(n = 10)
#> bin_names levels taxonomies confidences
#> 1 Otu001 1 Bacteria 100
#> 2 Otu001 2 "Bacteroidetes" 100
#> 3 Otu001 3 "Bacteroidia" 100
#> 4 Otu001 4 "Bacteroidales" 100
#> 5 Otu001 5 "Porphyromonadaceae" 100
#> 6 Otu001 6 "Porphyromonadaceae"_unclassified 100
#> 7 Otu002 1 Bacteria 100
#> 8 Otu002 2 "Bacteroidetes" 100
#> 9 Otu002 3 "Bacteroidia" 100
#> 10 Otu002 4 "Bacteroidales" 100
# To get the 'otu' bin representative sequences
report(
data = miseq, type = "bin_representatives",
bin_type = "otu"
) |> head(n = 5)
#> otu_names representative_names
#> 1 Otu001 M00967_43_000000000-A3JHG_1_1108_14299_17220
#> 2 Otu002 M00967_43_000000000-A3JHG_1_1106_22705_6123
#> 3 Otu003 M00967_43_000000000-A3JHG_1_1101_15533_5293
#> 4 Otu004 M00967_43_000000000-A3JHG_1_1105_25642_17588
#> 5 Otu005 M00967_43_000000000-A3JHG_1_2102_7041_13746
#> representative_sequences
#> 1 TAC--GT-AG-GGG--GCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GA-GC-G-TA-GAC-G-G-C-TG-T-G-C-AA-G-T-C-T-G-A-A-G--TG-A-AA-TG-C-C-GG-GG--CT-C-AA-C-C-C-C-G-G-A-ACT-G-C-TTTG-GAAAC-TG-T-ACAGC-TAGA-GT-GC-AG-GA-G-G---GG-T-G-AGCGGAATTCCTAGTGT-AGCGGT-GAAATGCGTAG-AT-A-TT-AG-GA-GG-AACACCGGT-GGCGAAGGCG------GCTCA-CTG-G-AC-TG-T-A-ACTGACG-TTGA-GGCT-CGAAA-GCG-TGGGG-AGC-AAACAGG
#> 2 TAC--GT-AG-GGG--GCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GA-GC-G-CA-GAC-G-G-C-TG-T-G-C-AA-G-T-C-T-G-G-A-G--TG-A-AA-GG-C-G-GG-GG--CC-C-AA-C-C-C-C-C-G-G-ACT-G-C-TCTG-GAAAC-TG-T-AAAGC-TGGA-GT-GC-AG-GA-G-A---GG-T-A-AGCGGAATTCCTAGTGT-AGCGGT-GAAATGCGTAG-AT-A-TT-AG-GA-GG-AACACCAGT-GGCGAAGGCG------GCTTA-CTG-G-AC-TG-C-A-ACTGACG-TTGA-GGCT-CGAAA-GCG-TGGGT-ATC-GAACAGG
#> 3 TAC--GG-AG-GAT--GCG-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GA-GC-G-TA-GAC-G-G-C-GA-T-G-C-AA-G-T-C-T-G-A-A-G--TG-A-AA-GG-C-G-GG-GG--CC-C-AA-C-C-C-C-C-G-G-ACT-G-C-TTTG-GAAAC-TG-T-ATAGC-TGGA-GT-GC-AG-GA-G-A---GG-T-A-AGTGGAATTCCTAGTGT-AGCGGT-GAAATGCGTAG-AT-A-TT-AG-GA-GG-AACACCAGT-GGCGAAGGCG------GCTTA-CTG-G-AC-TG-T-A-ACTGACG-TTGA-GGCT-CGAAA-GCG-TGGGG-AGC-AAACAGG
#> 4 TAC--GT-AG-GTG--GCA-A-G-C-G-T-T--AT-C-CGG-AT--TT-A-C-T--GG-GT--GT-A-AA-GG-GC-GT-G-TA-GGC-G-G-G-AC-T-G-C-AA-G-T-C-A-G-A-T-G--TG-A-AA-CC-C-A-TG-GG--CT-C-AA-C-C-C-A-T-G-G-CCT-G-C-ATTT-GAAAC-TG-T-AGTTC-TTGA-GT-GA-TG-GA-G-A---GG-C-A-GGCGGAATTCCGTGTGT-AGCGGT-GAAATGCGTAG-AT-A-TA-CG-GA-GG-AACACCAGT-GGCGAAGGCG------GCCTG-CTG-G-AC-AT-T-A-ACTGACG-CTGA-GGCG-CGAAA-GCG-TGGGG-AGC-AAACAGG
#> 5 TAC--GT-AG-GGG--GCG-A-G-C-G-T-T--AT-C-CGG-AT--TC-A-T-T--GG-GC--GT-A-AA-GC-GC-GC-G-CA-GGC-G-G-A-CT-C-A-T-AA-G-C-G-G-A-G-C-C--TT-T-AA-TC-T-T-GG-GG--CT-T-AA-C-C-T-C-A-A-G-T-C-G-G-GCCC-CGAAC-TG-T-GAGTC-TCGA-GT-GT-GG-TA-G-G---GG-A-A-GGCGGAATTCCCGGTGT-AGCGGT-GGAATGCGCAG-AT-A-TC-GG-GA-AG-AACACCGAT-GGCGAAGGCA------GCCTT-CTG-G-GC-CA-T-C-ACTGACG-CTGA-GGCG-CGAAA-GCT-AGGGG-AGC-AAACAGG
# To get a report about the sequences removed during your analysis:
report(data = miseq, type = "sequence_scrap")
#> data frame with 0 columns and 0 rows
# To get a report about the "otu" bins removed during your analysis:
report(data = miseq, type = "bin_scrap", bin_type = "otu")
#> data frame with 0 columns and 0 rows
# To get the metadata associated with your data:
metadata <- report(data = miseq, type = "metadata")
# To get the resource references associated with your data:
references <- report(data = miseq, type = "references")
# To get our custom report containing the contigs assembly data:
report(data = miseq, type = "contigs_report") |> head(n = 10)
#> Name Length Overlap_Length
#> 1 M00967_43_000000000-A3JHG_1_2101_16474_12783 253 250
#> 2 M00967_43_000000000-A3JHG_1_1113_12711_3318 253 249
#> 3 M00967_43_000000000-A3JHG_1_2108_14707_9807 253 249
#> 4 M00967_43_000000000-A3JHG_1_1110_4126_16552 252 249
#> 5 M00967_43_000000000-A3JHG_1_2102_8408_13436 253 249
#> 6 M00967_43_000000000-A3JHG_1_1107_22580_21773 252 250
#> 7 M00967_43_000000000-A3JHG_1_1108_14299_17220 253 249
#> 8 M00967_43_000000000-A3JHG_1_1114_8059_18290 253 249
#> 9 M00967_43_000000000-A3JHG_1_2112_9811_9982 253 249
#> 10 M00967_43_000000000-A3JHG_1_2103_25452_6018 252 249
#> Overlap_Start Overlap_End MisMatches Num_Ns Expected_Errors
#> 1 2 252 19 0 0.29461400
#> 2 2 251 0 0 0.00183396
#> 3 2 251 0 0 0.00196774
#> 4 2 251 4 0 0.05629750
#> 5 2 251 0 0 0.00259554
#> 6 1 251 8 0 0.05068300
#> 7 2 251 0 0 0.00215398
#> 8 3 252 11 0 0.05362360
#> 9 2 251 0 0 0.00184906
#> 10 2 251 18 0 0.54816100