Rarefy a phyloseq object, optionally averaging over repetitions
Source:R/normalize_pq.R
rarefy_pq.Rd
Wrapper around phyloseq::rarefy_even_depth() that can repeat the
rarefaction n times and return the averaged OTU table, reducing the
stochasticity of a single subsampling pass. With n = 1 (default) the
behaviour matches a standard single rarefaction.
Arguments
- physeq
(required) a
phyloseq-classobject obtained using thephyloseqpackage.- sample_size
(integer) the depth to rarefy to. If
NULL(default), the minimumsample_sums(physeq)is used.- n
(integer, default 1) number of rarefaction repetitions to average over. Values > 1 return a non-integer (averaged) OTU table.
- seed
(integer, default 123) random seed passed to
phyloseq::rarefy_even_depth().- ...
Additional arguments passed on to
phyloseq::rarefy_even_depth().
Value
A new phyloseq-class object with a
rarefied (or averaged-rarefied) otu_table.
Examples
data_f_rar <- rarefy_pq(data_fungi_mini, seed = 1)
sample_sums(data_f_rar)
#> A10-005-B_S188_MERGED.fastq.gz A10-005-H_S189_MERGED.fastq.gz
#> 1 1
#> A10-005-M_S190_MERGED.fastq.gz A12-007_S191_MERGED.fastq.gz
#> 1 1
#> A12-007-B_S2_MERGED.fastq.gz A15-004_S3_MERGED.fastq.gz
#> 1 1
#> A8-005_S4_MERGED.fastq.gz AB29-ABMX-H_S6_MERGED.fastq.gz
#> 1 1
#> AC27-013_S7_MERGED.fastq.gz AC29033_S8_MERGED.fastq.gz
#> 1 1
#> AD26-005-B_S9_MERGED.fastq.gz AD26-005-H_S10_MERGED.fastq.gz
#> 1 1
#> AD26-005-M_S11_MERGED.fastq.gz AD30-ABMX-M_S12_MERGED.fastq.gz
#> 1 1
#> AD32-007-M_S13_MERGED.fastq.gz ADABM30X-B_S14_MERGED.fastq.gz
#> 1 1
#> ADABM30X-H_S15_MERGED.fastq.gz ADABM30X-M_S16_MERGED.fastq.gz
#> 1 1
#> AE30-ABM507_S17_MERGED.fastq.gz B17-014_S18_MERGED.fastq.gz
#> 1 1
#> B18-006-B_S19_MERGED.fastq.gz BA16-036bis_S20_MERGED.fastq.gz
#> 1 1
#> BA17-050-B_S21_MERGED.fastq.gz BB19-006-H_S22_MERGED.fastq.gz
#> 1 1
#> BB6-019-M_S25_MERGED.fastq.gz BD14-021_S26_MERGED.fastq.gz
#> 1 1
#> BG7-010-H_S31_MERGED.fastq.gz BH9-021_S33_MERGED.fastq.gz
#> 1 1
#> BJ17-007-M_S34_MERGED.fastq.gz BJ8-ABM-003_S35_MERGED.fastq.gz
#> 1 1
#> BL7-006-H_S37_MERGED.fastq.gz BN11-041_S39_MERGED.fastq.gz
#> 1 1
#> BO8-002_S41_MERGED.fastq.gz BO8-005_S42_MERGED.fastq.gz
#> 1 1
#> BP11-001-B_S43_MERGED.fastq.gz BP11-001-H_S44_MERGED.fastq.gz
#> 1 1
#> BP11-001-M_S45_MERGED.fastq.gz BP12-025-B_S46_MERGED.fastq.gz
#> 1 1
#> BP14-006_S47_MERGED.fastq.gz BQ3-019_S48_MERGED.fastq.gz
#> 1 1
#> BQ4-018-B_S49_MERGED.fastq.gz BQ4-018-H_S50_MERGED.fastq.gz
#> 1 1
#> BQ4-018-M_S51_MERGED.fastq.gz BQ9ABM-002_S52_MERGED.fastq.gz
#> 1 1
#> BR8-005_S53_MERGED.fastq.gz BS14-006_S54_MERGED.fastq.gz
#> 1 1
#> BT-006-M_S55_MERGED.fastq.gz BT7-006_S56_MERGED.fastq.gz
#> 1 1
#> BV11-002-B_S57_MERGED.fastq.gz BV11-002-H_S58_MERGED.fastq.gz
#> 1 1
#> BV11-002-M_S59_MERGED.fastq.gz BW8-003_S60_MERGED.fastq.gz
#> 1 1
#> C1-001_S61_MERGED.fastq.gz C21-NV1-B_S62_MERGED.fastq.gz
#> 1 1
#> C9-005_S65_MERGED.fastq.gz CA9-X_S68_MERGED.fastq.gz
#> 1 1
#> CB8-019-B_S69_MERGED.fastq.gz CB8-019-H_S70_MERGED.fastq.gz
#> 1 1
#> CB8-019-M_S71_MERGED.fastq.gz CB9-013_S72_MERGED.fastq.gz
#> 1 1
#> CC3-044_S73_MERGED.fastq.gz D17-011_S77_MERGED.fastq.gz
#> 1 1
#> D18-003-B_S78_MERGED.fastq.gz D18-003-M_S80_MERGED.fastq.gz
#> 1 1
#> D22-NVABM1_S81_MERGED.fastq.gz D61-010-B_S82_MERGED.fastq.gz
#> 1 1
#> D9-027-H_S84_MERGED.fastq.gz D9-027-M_S85_MERGED.fastq.gz
#> 1 1
#> DBM-ABM-001_S86_MERGED.fastq.gz DJ2-008-H_S88_MERGED.fastq.gz
#> 1 1
#> DP4-ABM001_S90_MERGED.fastq.gz DS1-ABM002-B_S91_MERGED.fastq.gz
#> 1 1
#> DS1-ABM002-H_S92_MERGED.fastq.gz DS1-ABM002-M_S93_MERGED.fastq.gz
#> 1 1
#> DU3-045-B_S94_MERGED.fastq.gz DW4-007_S95_MERGED.fastq.gz
#> 1 1
#> DY5-004-B_S96_MERGED.fastq.gz DY5-004-H_S97_MERGED.fastq.gz
#> 1 1
#> DZ6-ABM-001_S99_MERGED.fastq.gz EA5-ABM-001_S103_MERGED.fastq.gz
#> 1 1
#> EC2-013-B_S104_MERGED.fastq.gz F6-ABM-001_S105_MERGED.fastq.gz
#> 1 1
#> F7-015-M_S106_MERGED.fastq.gz FOMES19-H_S108_MERGED.fastq.gz
#> 1 1
#> FOMES19-M_S109_MERGED.fastq.gz H10-018-M_S110_MERGED.fastq.gz
#> 1 1
#> H24-NVABM1-H_S111_MERGED.fastq.gz J18-004-B_S114_MERGED.fastq.gz
#> 1 1
#> J18-004-M_S116_MERGED.fastq.gz K18-002-H_S117_MERGED.fastq.gz
#> 1 1
#> K26-NVABM1_S118_MERGED.fastq.gz L19X-B_S119_MERGED.fastq.gz
#> 1 1
#> L19X-H_S120_MERGED.fastq.gz L19X-M_S121_MERGED.fastq.gz
#> 1 1
#> L23-002-B_S122_MERGED.fastq.gz L23-002-H_S123_MERGED.fastq.gz
#> 1 1
#> L23-002-M_S124_MERGED.fastq.gz N19X-H_S127_MERGED.fastq.gz
#> 1 1
#> N19X-M_S128_MERGED.fastq.gz N23-002-B_S130_MERGED.fastq.gz
#> 1 1
#> N23-002-H_S131_MERGED.fastq.gz N25-ABMX_S133_MERGED.fastq.gz
#> 1 1
#> NVABM-0058_S134_MERGED.fastq.gz NVABM-0163-H_S135_MERGED.fastq.gz
#> 1 1
#> NVABM-0397_S138_MERGED.fastq.gz NVABM0216_S136_MERGED.fastq.gz
#> 1 1
#> NVABM0244-M_S137_MERGED.fastq.gz O20-X-H_S140_MERGED.fastq.gz
#> 1 1
#> O20-X-M_S141_MERGED.fastq.gz O24-003-B_S145_MERGED.fastq.gz
#> 1 1
#> O26-004-B_S148_MERGED.fastq.gz O27-012_S151_MERGED.fastq.gz
#> 1 1
#> O9-005-B_S152_MERGED.fastq.gz P19-023-M_S153_MERGED.fastq.gz
#> 1 1
#> P27-015-M_S154_MERGED.fastq.gz P27-ABM001_S155_MERGED.fastq.gz
#> 1 1
#> Q27-ABM003-B_S156_MERGED.fastq.gz R25-ABMX_S157_MERGED.fastq.gz
#> 1 1
#> T28-011_S161_MERGED.fastq.gz T28-ABM602-B_S162_MERGED.fastq.gz
#> 1 1
#> U27-ABM002_S163_MERGED.fastq.gz W25-ABMX_S164_MERGED.fastq.gz
#> 1 1
#> W26-001-B_S165_MERGED.fastq.gz W30-006_S168_MERGED.fastq.gz
#> 1 1
#> W9-025-M_S169_MERGED.fastq.gz X24-009-B_S170_MERGED.fastq.gz
#> 1 1
#> X24-009-H_S171_MERGED.fastq.gz X24-009-M_S172_MERGED.fastq.gz
#> 1 1
#> X24-010_S173_MERGED.fastq.gz X29-004-B_S174_MERGED.fastq.gz
#> 1 1
#> X29-004-H_S175_MERGED.fastq.gz X29-004-M_S176_MERGED.fastq.gz
#> 1 1
#> Y21-ABM484-H_S177_MERGED.fastq.gz Y28-002-B_S178_MERGED.fastq.gz
#> 1 1
#> Y31-ABM484-B_S184_MERGED.fastq.gz Z29-001-H_S185_MERGED.fastq.gz
#> 1 1
#> Z30-ABM560-M_S187_MERGED.fastq.gz
#> 1
data_f_rar5 <- rarefy_pq(data_fungi_mini, n = 5, seed = 1)
sample_sums(data_f_rar5)
#> A10-005-B_S188_MERGED.fastq.gz A10-005-H_S189_MERGED.fastq.gz
#> 1 1
#> A10-005-M_S190_MERGED.fastq.gz A12-007_S191_MERGED.fastq.gz
#> 1 1
#> A12-007-B_S2_MERGED.fastq.gz A15-004_S3_MERGED.fastq.gz
#> 1 1
#> A8-005_S4_MERGED.fastq.gz AB29-ABMX-H_S6_MERGED.fastq.gz
#> 1 1
#> AC27-013_S7_MERGED.fastq.gz AC29033_S8_MERGED.fastq.gz
#> 1 1
#> AD26-005-B_S9_MERGED.fastq.gz AD26-005-H_S10_MERGED.fastq.gz
#> 1 1
#> AD26-005-M_S11_MERGED.fastq.gz AD30-ABMX-M_S12_MERGED.fastq.gz
#> 1 1
#> AD32-007-M_S13_MERGED.fastq.gz ADABM30X-B_S14_MERGED.fastq.gz
#> 1 1
#> ADABM30X-H_S15_MERGED.fastq.gz ADABM30X-M_S16_MERGED.fastq.gz
#> 1 1
#> AE30-ABM507_S17_MERGED.fastq.gz B17-014_S18_MERGED.fastq.gz
#> 1 1
#> B18-006-B_S19_MERGED.fastq.gz BA16-036bis_S20_MERGED.fastq.gz
#> 1 1
#> BA17-050-B_S21_MERGED.fastq.gz BB19-006-H_S22_MERGED.fastq.gz
#> 1 1
#> BB6-019-M_S25_MERGED.fastq.gz BD14-021_S26_MERGED.fastq.gz
#> 1 1
#> BG7-010-H_S31_MERGED.fastq.gz BH9-021_S33_MERGED.fastq.gz
#> 1 1
#> BJ17-007-M_S34_MERGED.fastq.gz BJ8-ABM-003_S35_MERGED.fastq.gz
#> 1 1
#> BL7-006-H_S37_MERGED.fastq.gz BN11-041_S39_MERGED.fastq.gz
#> 1 1
#> BO8-002_S41_MERGED.fastq.gz BO8-005_S42_MERGED.fastq.gz
#> 1 1
#> BP11-001-B_S43_MERGED.fastq.gz BP11-001-H_S44_MERGED.fastq.gz
#> 1 1
#> BP11-001-M_S45_MERGED.fastq.gz BP12-025-B_S46_MERGED.fastq.gz
#> 1 1
#> BP14-006_S47_MERGED.fastq.gz BQ3-019_S48_MERGED.fastq.gz
#> 1 1
#> BQ4-018-B_S49_MERGED.fastq.gz BQ4-018-H_S50_MERGED.fastq.gz
#> 1 1
#> BQ4-018-M_S51_MERGED.fastq.gz BQ9ABM-002_S52_MERGED.fastq.gz
#> 1 1
#> BR8-005_S53_MERGED.fastq.gz BS14-006_S54_MERGED.fastq.gz
#> 1 1
#> BT-006-M_S55_MERGED.fastq.gz BT7-006_S56_MERGED.fastq.gz
#> 1 1
#> BV11-002-B_S57_MERGED.fastq.gz BV11-002-H_S58_MERGED.fastq.gz
#> 1 1
#> BV11-002-M_S59_MERGED.fastq.gz BW8-003_S60_MERGED.fastq.gz
#> 1 1
#> C1-001_S61_MERGED.fastq.gz C21-NV1-B_S62_MERGED.fastq.gz
#> 1 1
#> C9-005_S65_MERGED.fastq.gz CA9-X_S68_MERGED.fastq.gz
#> 1 1
#> CB8-019-B_S69_MERGED.fastq.gz CB8-019-H_S70_MERGED.fastq.gz
#> 1 1
#> CB8-019-M_S71_MERGED.fastq.gz CB9-013_S72_MERGED.fastq.gz
#> 1 1
#> CC3-044_S73_MERGED.fastq.gz D17-011_S77_MERGED.fastq.gz
#> 1 1
#> D18-003-B_S78_MERGED.fastq.gz D18-003-M_S80_MERGED.fastq.gz
#> 1 1
#> D22-NVABM1_S81_MERGED.fastq.gz D61-010-B_S82_MERGED.fastq.gz
#> 1 1
#> D9-027-H_S84_MERGED.fastq.gz D9-027-M_S85_MERGED.fastq.gz
#> 1 1
#> DBM-ABM-001_S86_MERGED.fastq.gz DJ2-008-H_S88_MERGED.fastq.gz
#> 1 1
#> DP4-ABM001_S90_MERGED.fastq.gz DS1-ABM002-B_S91_MERGED.fastq.gz
#> 1 1
#> DS1-ABM002-H_S92_MERGED.fastq.gz DS1-ABM002-M_S93_MERGED.fastq.gz
#> 1 1
#> DU3-045-B_S94_MERGED.fastq.gz DW4-007_S95_MERGED.fastq.gz
#> 1 1
#> DY5-004-B_S96_MERGED.fastq.gz DY5-004-H_S97_MERGED.fastq.gz
#> 1 1
#> DZ6-ABM-001_S99_MERGED.fastq.gz EA5-ABM-001_S103_MERGED.fastq.gz
#> 1 1
#> EC2-013-B_S104_MERGED.fastq.gz F6-ABM-001_S105_MERGED.fastq.gz
#> 1 1
#> F7-015-M_S106_MERGED.fastq.gz FOMES19-H_S108_MERGED.fastq.gz
#> 1 1
#> FOMES19-M_S109_MERGED.fastq.gz H10-018-M_S110_MERGED.fastq.gz
#> 1 1
#> H24-NVABM1-H_S111_MERGED.fastq.gz J18-004-B_S114_MERGED.fastq.gz
#> 1 1
#> J18-004-M_S116_MERGED.fastq.gz K18-002-H_S117_MERGED.fastq.gz
#> 1 1
#> K26-NVABM1_S118_MERGED.fastq.gz L19X-B_S119_MERGED.fastq.gz
#> 1 1
#> L19X-H_S120_MERGED.fastq.gz L19X-M_S121_MERGED.fastq.gz
#> 1 1
#> L23-002-B_S122_MERGED.fastq.gz L23-002-H_S123_MERGED.fastq.gz
#> 1 1
#> L23-002-M_S124_MERGED.fastq.gz N19X-H_S127_MERGED.fastq.gz
#> 1 1
#> N19X-M_S128_MERGED.fastq.gz N23-002-B_S130_MERGED.fastq.gz
#> 1 1
#> N23-002-H_S131_MERGED.fastq.gz N25-ABMX_S133_MERGED.fastq.gz
#> 1 1
#> NVABM-0058_S134_MERGED.fastq.gz NVABM-0163-H_S135_MERGED.fastq.gz
#> 1 1
#> NVABM-0397_S138_MERGED.fastq.gz NVABM0216_S136_MERGED.fastq.gz
#> 1 1
#> NVABM0244-M_S137_MERGED.fastq.gz O20-X-H_S140_MERGED.fastq.gz
#> 1 1
#> O20-X-M_S141_MERGED.fastq.gz O24-003-B_S145_MERGED.fastq.gz
#> 1 1
#> O26-004-B_S148_MERGED.fastq.gz O27-012_S151_MERGED.fastq.gz
#> 1 1
#> O9-005-B_S152_MERGED.fastq.gz P19-023-M_S153_MERGED.fastq.gz
#> 1 1
#> P27-015-M_S154_MERGED.fastq.gz P27-ABM001_S155_MERGED.fastq.gz
#> 1 1
#> Q27-ABM003-B_S156_MERGED.fastq.gz R25-ABMX_S157_MERGED.fastq.gz
#> 1 1
#> T28-011_S161_MERGED.fastq.gz T28-ABM602-B_S162_MERGED.fastq.gz
#> 1 1
#> U27-ABM002_S163_MERGED.fastq.gz W25-ABMX_S164_MERGED.fastq.gz
#> 1 1
#> W26-001-B_S165_MERGED.fastq.gz W30-006_S168_MERGED.fastq.gz
#> 1 1
#> W9-025-M_S169_MERGED.fastq.gz X24-009-B_S170_MERGED.fastq.gz
#> 1 1
#> X24-009-H_S171_MERGED.fastq.gz X24-009-M_S172_MERGED.fastq.gz
#> 1 1
#> X24-010_S173_MERGED.fastq.gz X29-004-B_S174_MERGED.fastq.gz
#> 1 1
#> X29-004-H_S175_MERGED.fastq.gz X29-004-M_S176_MERGED.fastq.gz
#> 1 1
#> Y21-ABM484-H_S177_MERGED.fastq.gz Y28-002-B_S178_MERGED.fastq.gz
#> 1 1
#> Y31-ABM484-B_S184_MERGED.fastq.gz Z29-001-H_S185_MERGED.fastq.gz
#> 1 1
#> Z30-ABM560-M_S187_MERGED.fastq.gz
#> 1