Geometric Mean of Pairwise Ratios (GMPR) normalization of a phyloseq object
Source:R/normalize_pq.R
gmpr_pq.Rd
Pure-R implementation of the Geometric Mean of Pairwise Ratios normalization (Chen et al. 2018, doi:10.7717/peerj.4600 ) tailored for zero-inflated count tables such as microbial OTU tables. Returns counts divided by the per-sample GMPR size factors.
Arguments
- physeq
(required) a
phyloseq-classobject obtained using thephyloseqpackage.- intersect_no
(integer, default 4) minimum number of shared taxa between two samples for the pairwise ratio to be computed.
- ct_min
(integer, default 2) minimum count for a taxon to be considered "shared" between two samples.
Value
A new phyloseq-class object with a
GMPR-normalised otu_table. Size factors are stored as an attribute
"gmpr_size_factors" on the otu_table.
References
Chen L. et al. (2018) GMPR: a robust normalization method for zero-inflated count data with application to microbiome sequencing data. PeerJ 6:e4600. doi:10.7717/peerj.4600
Examples
data_f_gmpr <- gmpr_pq(data_fungi_mini)
#> Warning: GMPR size factors could not be computed for 90 sample(s); these samples are left unscaled.
sample_sums(data_f_gmpr)
#> A10-005-B_S188_MERGED.fastq.gz A10-005-H_S189_MERGED.fastq.gz
#> 1506.3028 10201.0000
#> A10-005-M_S190_MERGED.fastq.gz A12-007_S191_MERGED.fastq.gz
#> 2163.9241 10267.8240
#> A12-007-B_S2_MERGED.fastq.gz A15-004_S3_MERGED.fastq.gz
#> 1869.0000 17.0000
#> A8-005_S4_MERGED.fastq.gz AB29-ABMX-H_S6_MERGED.fastq.gz
#> 1736.0591 1806.0000
#> AC27-013_S7_MERGED.fastq.gz AC29033_S8_MERGED.fastq.gz
#> 8247.0000 54.0000
#> AD26-005-B_S9_MERGED.fastq.gz AD26-005-H_S10_MERGED.fastq.gz
#> 18.0000 4719.0000
#> AD26-005-M_S11_MERGED.fastq.gz AD30-ABMX-M_S12_MERGED.fastq.gz
#> 3615.0000 592.0000
#> AD32-007-M_S13_MERGED.fastq.gz ADABM30X-B_S14_MERGED.fastq.gz
#> 796.3391 6982.0863
#> ADABM30X-H_S15_MERGED.fastq.gz ADABM30X-M_S16_MERGED.fastq.gz
#> 1187.6686 894.0000
#> AE30-ABM507_S17_MERGED.fastq.gz B17-014_S18_MERGED.fastq.gz
#> 1655.0000 6670.9711
#> B18-006-B_S19_MERGED.fastq.gz BA16-036bis_S20_MERGED.fastq.gz
#> 233.0000 38335.0000
#> BA17-050-B_S21_MERGED.fastq.gz BB19-006-H_S22_MERGED.fastq.gz
#> 3165.6960 21861.0000
#> BB6-019-M_S25_MERGED.fastq.gz BD14-021_S26_MERGED.fastq.gz
#> 2206.2171 906.6284
#> BG7-010-H_S31_MERGED.fastq.gz BH9-021_S33_MERGED.fastq.gz
#> 1.0000 1.0000
#> BJ17-007-M_S34_MERGED.fastq.gz BJ8-ABM-003_S35_MERGED.fastq.gz
#> 61090.7241 1360.0000
#> BL7-006-H_S37_MERGED.fastq.gz BN11-041_S39_MERGED.fastq.gz
#> 2.0000 22649.5899
#> BO8-002_S41_MERGED.fastq.gz BO8-005_S42_MERGED.fastq.gz
#> 695.0000 1.0000
#> BP11-001-B_S43_MERGED.fastq.gz BP11-001-H_S44_MERGED.fastq.gz
#> 3316.0000 1508.8342
#> BP11-001-M_S45_MERGED.fastq.gz BP12-025-B_S46_MERGED.fastq.gz
#> 15602.0000 1.0000
#> BP14-006_S47_MERGED.fastq.gz BQ3-019_S48_MERGED.fastq.gz
#> 1666.5322 1.0000
#> BQ4-018-B_S49_MERGED.fastq.gz BQ4-018-H_S50_MERGED.fastq.gz
#> 9898.0000 8929.0000
#> BQ4-018-M_S51_MERGED.fastq.gz BQ9ABM-002_S52_MERGED.fastq.gz
#> 440.0000 15818.0000
#> BR8-005_S53_MERGED.fastq.gz BS14-006_S54_MERGED.fastq.gz
#> 1.0000 5999.7248
#> BT-006-M_S55_MERGED.fastq.gz BT7-006_S56_MERGED.fastq.gz
#> 109.0000 43.0000
#> BV11-002-B_S57_MERGED.fastq.gz BV11-002-H_S58_MERGED.fastq.gz
#> 3018.0074 681.0978
#> BV11-002-M_S59_MERGED.fastq.gz BW8-003_S60_MERGED.fastq.gz
#> 23.0000 4189.6647
#> C1-001_S61_MERGED.fastq.gz C21-NV1-B_S62_MERGED.fastq.gz
#> 3342.0391 82.0000
#> C9-005_S65_MERGED.fastq.gz CA9-X_S68_MERGED.fastq.gz
#> 1491.0000 1207.2588
#> CB8-019-B_S69_MERGED.fastq.gz CB8-019-H_S70_MERGED.fastq.gz
#> 1.0000 1.0000
#> CB8-019-M_S71_MERGED.fastq.gz CB9-013_S72_MERGED.fastq.gz
#> 2.0000 5236.2514
#> CC3-044_S73_MERGED.fastq.gz D17-011_S77_MERGED.fastq.gz
#> 1193.5960 20487.0585
#> D18-003-B_S78_MERGED.fastq.gz D18-003-M_S80_MERGED.fastq.gz
#> 3395.2792 68.0000
#> D22-NVABM1_S81_MERGED.fastq.gz D61-010-B_S82_MERGED.fastq.gz
#> 13780.8455 18890.0000
#> D9-027-H_S84_MERGED.fastq.gz D9-027-M_S85_MERGED.fastq.gz
#> 3.0000 1.0000
#> DBM-ABM-001_S86_MERGED.fastq.gz DJ2-008-H_S88_MERGED.fastq.gz
#> 1123.4650 51.0000
#> DP4-ABM001_S90_MERGED.fastq.gz DS1-ABM002-B_S91_MERGED.fastq.gz
#> 7125.0000 13.0000
#> DS1-ABM002-H_S92_MERGED.fastq.gz DS1-ABM002-M_S93_MERGED.fastq.gz
#> 2434.0000 41.0000
#> DU3-045-B_S94_MERGED.fastq.gz DW4-007_S95_MERGED.fastq.gz
#> 55241.2897 11080.0000
#> DY5-004-B_S96_MERGED.fastq.gz DY5-004-H_S97_MERGED.fastq.gz
#> 7.0000 1.0000
#> DZ6-ABM-001_S99_MERGED.fastq.gz EA5-ABM-001_S103_MERGED.fastq.gz
#> 2307.0000 6113.0000
#> EC2-013-B_S104_MERGED.fastq.gz F6-ABM-001_S105_MERGED.fastq.gz
#> 8118.0000 571.0000
#> F7-015-M_S106_MERGED.fastq.gz FOMES19-H_S108_MERGED.fastq.gz
#> 520.0000 2552.0000
#> FOMES19-M_S109_MERGED.fastq.gz H10-018-M_S110_MERGED.fastq.gz
#> 6398.0000 1.0000
#> H24-NVABM1-H_S111_MERGED.fastq.gz J18-004-B_S114_MERGED.fastq.gz
#> 115.0000 1.0000
#> J18-004-M_S116_MERGED.fastq.gz K18-002-H_S117_MERGED.fastq.gz
#> 4.0000 106.2525
#> K26-NVABM1_S118_MERGED.fastq.gz L19X-B_S119_MERGED.fastq.gz
#> 1875.5830 182.0000
#> L19X-H_S120_MERGED.fastq.gz L19X-M_S121_MERGED.fastq.gz
#> 1641.2297 3608.3115
#> L23-002-B_S122_MERGED.fastq.gz L23-002-H_S123_MERGED.fastq.gz
#> 5491.7380 994.0011
#> L23-002-M_S124_MERGED.fastq.gz N19X-H_S127_MERGED.fastq.gz
#> 189.0000 797.6245
#> N19X-M_S128_MERGED.fastq.gz N23-002-B_S130_MERGED.fastq.gz
#> 1113.5429 3.0000
#> N23-002-H_S131_MERGED.fastq.gz N25-ABMX_S133_MERGED.fastq.gz
#> 441.0000 19484.0000
#> NVABM-0058_S134_MERGED.fastq.gz NVABM-0163-H_S135_MERGED.fastq.gz
#> 10611.0000 177.0000
#> NVABM-0397_S138_MERGED.fastq.gz NVABM0216_S136_MERGED.fastq.gz
#> 50.0000 136.0000
#> NVABM0244-M_S137_MERGED.fastq.gz O20-X-H_S140_MERGED.fastq.gz
#> 2.0000 21324.6058
#> O20-X-M_S141_MERGED.fastq.gz O24-003-B_S145_MERGED.fastq.gz
#> 1234.8654 2.0000
#> O26-004-B_S148_MERGED.fastq.gz O27-012_S151_MERGED.fastq.gz
#> 21.0000 1.0000
#> O9-005-B_S152_MERGED.fastq.gz P19-023-M_S153_MERGED.fastq.gz
#> 3888.0000 57.0000
#> P27-015-M_S154_MERGED.fastq.gz P27-ABM001_S155_MERGED.fastq.gz
#> 475.0000 2.0000
#> Q27-ABM003-B_S156_MERGED.fastq.gz R25-ABMX_S157_MERGED.fastq.gz
#> 471.0000 1122.6977
#> T28-011_S161_MERGED.fastq.gz T28-ABM602-B_S162_MERGED.fastq.gz
#> 9390.0000 17.0000
#> U27-ABM002_S163_MERGED.fastq.gz W25-ABMX_S164_MERGED.fastq.gz
#> 2244.7856 203.0000
#> W26-001-B_S165_MERGED.fastq.gz W30-006_S168_MERGED.fastq.gz
#> 1.0000 29329.3969
#> W9-025-M_S169_MERGED.fastq.gz X24-009-B_S170_MERGED.fastq.gz
#> 2.0000 12526.4824
#> X24-009-H_S171_MERGED.fastq.gz X24-009-M_S172_MERGED.fastq.gz
#> 2270.0862 2036.6323
#> X24-010_S173_MERGED.fastq.gz X29-004-B_S174_MERGED.fastq.gz
#> 10756.0000 2.0000
#> X29-004-H_S175_MERGED.fastq.gz X29-004-M_S176_MERGED.fastq.gz
#> 1462.7702 12564.0000
#> Y21-ABM484-H_S177_MERGED.fastq.gz Y28-002-B_S178_MERGED.fastq.gz
#> 1194.0000 9.0000
#> Y31-ABM484-B_S184_MERGED.fastq.gz Z29-001-H_S185_MERGED.fastq.gz
#> 5674.1376 3.0000
#> Z30-ABM560-M_S187_MERGED.fastq.gz
#> 3760.1777