Add fake sequences by shuffling existing ones in a phyloseq object

Useful to compute true negative values with functions tc_metrics_mock() and tc_metrics_mock_vec().

Note the that the tax_table for additional sequences is full of NA and that the corresponding otu_table is full of 0.

Usage

add_shuffle_seq_pq(physeq, n_fake = NULL, prop_fake = NULL, prefix = "fake_")

Arguments

physeq: (required) A phyloseq-class object obtained using the phyloseq package.
n_fake: (integer, default NULL) A number of fake taxa to add. Must specify either n_fake or prop_fake, not both.
prop_fake: (numeric, default NULL) A proportion of fake taxa to add. Must specify either n_fake or prop_fake, not both.
prefix: (character, default "fake_") A prefix to add to the taxa name.

Value

A phyloseq object

Author

Adrien Taudière

Examples

d_fake_F <- data_fungi_mini |>
  add_shuffle_seq_pq(prop_fake = 0.1)
#> Taxa are now in columns.
#> Cleaning suppress 0 taxa (  ) and 122 sample(s) ( A10-005-H_S189_MERGED.fastq.gz / A12-007-B_S2_MERGED.fastq.gz / A15-004_S3_MERGED.fastq.gz / A8-005_S4_MERGED.fastq.gz / AB29-ABMX-H_S6_MERGED.fastq.gz / AC27-013_S7_MERGED.fastq.gz / AD26-005-B_S9_MERGED.fastq.gz / AD26-005-H_S10_MERGED.fastq.gz / AD26-005-M_S11_MERGED.fastq.gz / AD30-ABMX-M_S12_MERGED.fastq.gz / ADABM30X-B_S14_MERGED.fastq.gz / ADABM30X-M_S16_MERGED.fastq.gz / AE30-ABM507_S17_MERGED.fastq.gz / B18-006-B_S19_MERGED.fastq.gz / BA16-036bis_S20_MERGED.fastq.gz / BA17-050-B_S21_MERGED.fastq.gz / BB19-006-H_S22_MERGED.fastq.gz / BB6-019-M_S25_MERGED.fastq.gz / BD14-021_S26_MERGED.fastq.gz / BG7-010-H_S31_MERGED.fastq.gz / BH9-021_S33_MERGED.fastq.gz / BJ8-ABM-003_S35_MERGED.fastq.gz / BL7-006-H_S37_MERGED.fastq.gz / BN11-041_S39_MERGED.fastq.gz / BO8-002_S41_MERGED.fastq.gz / BO8-005_S42_MERGED.fastq.gz / BP11-001-B_S43_MERGED.fastq.gz / BP11-001-H_S44_MERGED.fastq.gz / BP11-001-M_S45_MERGED.fastq.gz / BP12-025-B_S46_MERGED.fastq.gz / BQ3-019_S48_MERGED.fastq.gz / BQ4-018-B_S49_MERGED.fastq.gz / BQ4-018-H_S50_MERGED.fastq.gz / BQ4-018-M_S51_MERGED.fastq.gz / BQ9ABM-002_S52_MERGED.fastq.gz / BR8-005_S53_MERGED.fastq.gz / BS14-006_S54_MERGED.fastq.gz / BT-006-M_S55_MERGED.fastq.gz / BT7-006_S56_MERGED.fastq.gz / BV11-002-B_S57_MERGED.fastq.gz / BV11-002-H_S58_MERGED.fastq.gz / BV11-002-M_S59_MERGED.fastq.gz / BW8-003_S60_MERGED.fastq.gz / C21-NV1-B_S62_MERGED.fastq.gz / C9-005_S65_MERGED.fastq.gz / CA9-X_S68_MERGED.fastq.gz / CB8-019-B_S69_MERGED.fastq.gz / CB8-019-H_S70_MERGED.fastq.gz / CB8-019-M_S71_MERGED.fastq.gz / CB9-013_S72_MERGED.fastq.gz / CC3-044_S73_MERGED.fastq.gz / D17-011_S77_MERGED.fastq.gz / D18-003-B_S78_MERGED.fastq.gz / D18-003-M_S80_MERGED.fastq.gz / D22-NVABM1_S81_MERGED.fastq.gz / D61-010-B_S82_MERGED.fastq.gz / D9-027-H_S84_MERGED.fastq.gz / D9-027-M_S85_MERGED.fastq.gz / DBM-ABM-001_S86_MERGED.fastq.gz / DJ2-008-H_S88_MERGED.fastq.gz / DP4-ABM001_S90_MERGED.fastq.gz / DS1-ABM002-B_S91_MERGED.fastq.gz / DS1-ABM002-H_S92_MERGED.fastq.gz / DS1-ABM002-M_S93_MERGED.fastq.gz / DU3-045-B_S94_MERGED.fastq.gz / DW4-007_S95_MERGED.fastq.gz / DY5-004-H_S97_MERGED.fastq.gz / EA5-ABM-001_S103_MERGED.fastq.gz / EC2-013-B_S104_MERGED.fastq.gz / F6-ABM-001_S105_MERGED.fastq.gz / F7-015-M_S106_MERGED.fastq.gz / FOMES19-H_S108_MERGED.fastq.gz / FOMES19-M_S109_MERGED.fastq.gz / H10-018-M_S110_MERGED.fastq.gz / H24-NVABM1-H_S111_MERGED.fastq.gz / J18-004-B_S114_MERGED.fastq.gz / J18-004-M_S116_MERGED.fastq.gz / K18-002-H_S117_MERGED.fastq.gz / K26-NVABM1_S118_MERGED.fastq.gz / L19X-B_S119_MERGED.fastq.gz / L19X-H_S120_MERGED.fastq.gz / L19X-M_S121_MERGED.fastq.gz / L23-002-B_S122_MERGED.fastq.gz / L23-002-H_S123_MERGED.fastq.gz / L23-002-M_S124_MERGED.fastq.gz / N19X-H_S127_MERGED.fastq.gz / N19X-M_S128_MERGED.fastq.gz / N23-002-B_S130_MERGED.fastq.gz / N23-002-H_S131_MERGED.fastq.gz / N25-ABMX_S133_MERGED.fastq.gz / NVABM-0058_S134_MERGED.fastq.gz / NVABM-0163-H_S135_MERGED.fastq.gz / NVABM-0397_S138_MERGED.fastq.gz / NVABM0216_S136_MERGED.fastq.gz / NVABM0244-M_S137_MERGED.fastq.gz / O20-X-H_S140_MERGED.fastq.gz / O20-X-M_S141_MERGED.fastq.gz / O24-003-B_S145_MERGED.fastq.gz / O26-004-B_S148_MERGED.fastq.gz / O27-012_S151_MERGED.fastq.gz / O9-005-B_S152_MERGED.fastq.gz / P19-023-M_S153_MERGED.fastq.gz / P27-015-M_S154_MERGED.fastq.gz / P27-ABM001_S155_MERGED.fastq.gz / Q27-ABM003-B_S156_MERGED.fastq.gz / R25-ABMX_S157_MERGED.fastq.gz / T28-011_S161_MERGED.fastq.gz / T28-ABM602-B_S162_MERGED.fastq.gz / U27-ABM002_S163_MERGED.fastq.gz / W25-ABMX_S164_MERGED.fastq.gz / W26-001-B_S165_MERGED.fastq.gz / W30-006_S168_MERGED.fastq.gz / W9-025-M_S169_MERGED.fastq.gz / X24-009-B_S170_MERGED.fastq.gz / X24-009-H_S171_MERGED.fastq.gz / X24-009-M_S172_MERGED.fastq.gz / X24-010_S173_MERGED.fastq.gz / Y21-ABM484-H_S177_MERGED.fastq.gz / Y28-002-B_S178_MERGED.fastq.gz / Y31-ABM484-B_S184_MERGED.fastq.gz / Z29-001-H_S185_MERGED.fastq.gz / Z30-ABM560-M_S187_MERGED.fastq.gz ).
#> Number of non-matching ASV 0
#> Number of matching ASV 45
#> Number of filtered-out ASV 41
#> Number of kept ASV 4
#> Number of kept samples 15
#> Taxa are now in rows.
ntaxa(d_fake_F) - ntaxa(data_fungi_mini)
#> [1] 4