Convert phyloseq OTU count data into DGEList for edgeR package
Source:R/Deseq2_edgeR.R
phyloseq_to_edgeR.RdConvert phyloseq OTU count data into DGEList for edgeR package
Arguments
- physeq
(required) a
phyloseq-classobject obtained using thephyloseqpackage.- group
(required) A character vector or factor giving the experimental group/condition for each sample/library. Alternatively, you may provide the name of a sample variable. This name should be among the output of
sample_variables(physeq), in which caseget_variable(physeq, group)would return either a character vector or factor. This is passed on toDGEList, and you may find further details or examples in its documentation.- method
The label of the edgeR-implemented normalization to use. See
calcNormFactorsfor supported options and details. The default option is"RLE", which is a scaling factor method proposed by Anders and Huber (2010). At time of writing, the edgeR package supported the following options to themethodargument:c("TMM", "RLE", "upperquartile", "none").- remove_na
(logical) If TRUE, samples with NA values in the group variable will be removed.
- ...
Additional arguments passed on to
DGEList
Value
A DGEList object. See edgeR::estimateTagwiseDisp() for more details.
Examples
# \donttest{
if (requireNamespace("edgeR")) {
phyloseq_to_edgeR(data_fungi_mini, group = "Height")
}
#> Loading required namespace: edgeR
#> An object of class "DGEList"
#> $counts
#> A10-005-B_S188_MERGED.fastq.gz A10-005-H_S189_MERGED.fastq.gz
#> ASV7 768 10188
#> ASV8 579 10
#> ASV12 1 2
#> ASV18 31 1
#> ASV25 1 1
#> A10-005-M_S190_MERGED.fastq.gz A12-007-B_S2_MERGED.fastq.gz
#> ASV7 264 1
#> ASV8 400 830
#> ASV12 1 1
#> ASV18 4 1041
#> ASV25 1 1
#> AB29-ABMX-H_S6_MERGED.fastq.gz AD26-005-B_S9_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 2 1
#> ASV12 2 1
#> ASV18 1 1
#> ASV25 1 1
#> AD26-005-H_S10_MERGED.fastq.gz AD26-005-M_S11_MERGED.fastq.gz
#> ASV7 1 2
#> ASV8 1 1
#> ASV12 1 1339
#> ASV18 1 1
#> ASV25 1 1
#> AD30-ABMX-M_S12_MERGED.fastq.gz AD32-007-M_S13_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 2 8
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 1
#> ADABM30X-B_S14_MERGED.fastq.gz ADABM30X-H_S15_MERGED.fastq.gz
#> ASV7 1 540
#> ASV8 3 3
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 3
#> ADABM30X-M_S16_MERGED.fastq.gz B18-006-B_S19_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 1 1
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 1
#> BA17-050-B_S21_MERGED.fastq.gz BB19-006-H_S22_MERGED.fastq.gz
#> ASV7 2885 1
#> ASV8 5 9742
#> ASV12 1 1
#> ASV18 1 11964
#> ASV25 1 1
#> BB6-019-M_S25_MERGED.fastq.gz BG7-010-H_S31_MERGED.fastq.gz
#> ASV7 874 1
#> ASV8 337 1
#> ASV12 1 1
#> ASV18 8 1
#> ASV25 1 1
#> BJ17-007-M_S34_MERGED.fastq.gz BL7-006-H_S37_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 7 3
#> ASV12 7 1
#> ASV18 1 1
#> ASV25 2 1
#> BP11-001-B_S43_MERGED.fastq.gz BP11-001-H_S44_MERGED.fastq.gz
#> ASV7 1 995
#> ASV8 2 9
#> ASV12 2 1
#> ASV18 1 1846
#> ASV25 1 1
#> BP11-001-M_S45_MERGED.fastq.gz BP12-025-B_S46_MERGED.fastq.gz
#> ASV7 7 1
#> ASV8 7 2
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 1
#> BQ4-018-B_S49_MERGED.fastq.gz BQ4-018-H_S50_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 2 2
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 2
#> BQ4-018-M_S51_MERGED.fastq.gz BT-006-M_S55_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 1 1
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 1
#> BV11-002-B_S57_MERGED.fastq.gz BV11-002-H_S58_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 4 3
#> ASV12 7551 1
#> ASV18 1 1
#> ASV25 1 67
#> BV11-002-M_S59_MERGED.fastq.gz C21-NV1-B_S62_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 1 1
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 1
#> CB8-019-B_S69_MERGED.fastq.gz CB8-019-H_S70_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 1 1
#> ASV12 2 1
#> ASV18 1 1
#> ASV25 1 1
#> CB8-019-M_S71_MERGED.fastq.gz D18-003-B_S78_MERGED.fastq.gz
#> ASV7 1 40
#> ASV8 1 32
#> ASV12 3 1
#> ASV18 1 1
#> ASV25 1 1
#> D18-003-M_S80_MERGED.fastq.gz D61-010-B_S82_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 1 6
#> ASV12 2 2
#> ASV18 1 1
#> ASV25 1 5
#> D9-027-H_S84_MERGED.fastq.gz D9-027-M_S85_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 4 2
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 1
#> DJ2-008-H_S88_MERGED.fastq.gz DS1-ABM002-B_S91_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 1 1
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 1
#> DS1-ABM002-H_S92_MERGED.fastq.gz DS1-ABM002-M_S93_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 1 1
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 2 4
#> DU3-045-B_S94_MERGED.fastq.gz DY5-004-B_S96_MERGED.fastq.gz
#> ASV7 34 1
#> ASV8 1109 1
#> ASV12 8 1
#> ASV18 8 1
#> ASV25 1 1
#> DY5-004-H_S97_MERGED.fastq.gz EC2-013-B_S104_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 1 2
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 1
#> F7-015-M_S106_MERGED.fastq.gz FOMES19-H_S108_MERGED.fastq.gz
#> ASV7 1 2
#> ASV8 1 1
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 1
#> FOMES19-M_S109_MERGED.fastq.gz H10-018-M_S110_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 1 2
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 1
#> H24-NVABM1-H_S111_MERGED.fastq.gz J18-004-B_S114_MERGED.fastq.gz
#> ASV7 105 1
#> ASV8 1 1
#> ASV12 3 1
#> ASV18 1 1
#> ASV25 10 2
#> J18-004-M_S116_MERGED.fastq.gz K18-002-H_S117_MERGED.fastq.gz
#> ASV7 1 36
#> ASV8 1 1
#> ASV12 1 1
#> ASV18 1 34
#> ASV25 1 1
#> L19X-B_S119_MERGED.fastq.gz L19X-H_S120_MERGED.fastq.gz
#> ASV7 1 336
#> ASV8 183 37
#> ASV12 1 1
#> ASV18 1 10
#> ASV25 1 1
#> L19X-M_S121_MERGED.fastq.gz L23-002-B_S122_MERGED.fastq.gz
#> ASV7 2801 7
#> ASV8 445 34
#> ASV12 1 1
#> ASV18 22 28
#> ASV25 1 1
#> L23-002-H_S123_MERGED.fastq.gz L23-002-M_S124_MERGED.fastq.gz
#> ASV7 2025 1
#> ASV8 2111 152
#> ASV12 1 1
#> ASV18 104 38
#> ASV25 1 1
#> N19X-H_S127_MERGED.fastq.gz N19X-M_S128_MERGED.fastq.gz
#> ASV7 1484 172
#> ASV8 2318 282
#> ASV12 1 1
#> ASV18 167 12
#> ASV25 1 1
#> N23-002-B_S130_MERGED.fastq.gz N23-002-H_S131_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 1 2
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 437
#> NVABM-0163-H_S135_MERGED.fastq.gz NVABM0244-M_S137_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 1 1
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 1
#> O20-X-H_S140_MERGED.fastq.gz O20-X-M_S141_MERGED.fastq.gz
#> ASV7 102 2111
#> ASV8 23 883
#> ASV12 1579 4
#> ASV18 4 70
#> ASV25 1 1
#> O24-003-B_S145_MERGED.fastq.gz O26-004-B_S148_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 3 1
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 1
#> O9-005-B_S152_MERGED.fastq.gz P19-023-M_S153_MERGED.fastq.gz
#> ASV7 1 2
#> ASV8 2 27
#> ASV12 2 1
#> ASV18 1 1
#> ASV25 1 1
#> P27-015-M_S154_MERGED.fastq.gz Q27-ABM003-B_S156_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 193 472
#> ASV12 8 1
#> ASV18 277 1
#> ASV25 1 1
#> T28-ABM602-B_S162_MERGED.fastq.gz W26-001-B_S165_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 1 1
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 1
#> W9-025-M_S169_MERGED.fastq.gz X24-009-B_S170_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 1 1
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 1
#> X24-009-H_S171_MERGED.fastq.gz X24-009-M_S172_MERGED.fastq.gz
#> ASV7 2 1
#> ASV8 6 8
#> ASV12 1 1
#> ASV18 1 1
#> ASV25 1 1
#> X29-004-B_S174_MERGED.fastq.gz X29-004-H_S175_MERGED.fastq.gz
#> ASV7 1 108
#> ASV8 1 113
#> ASV12 1 1
#> ASV18 1 2
#> ASV25 1 1
#> X29-004-M_S176_MERGED.fastq.gz Y21-ABM484-H_S177_MERGED.fastq.gz
#> ASV7 1 1
#> ASV8 3 2
#> ASV12 1 250
#> ASV18 1 1
#> ASV25 1 1
#> Y28-002-B_S178_MERGED.fastq.gz Y31-ABM484-B_S184_MERGED.fastq.gz
#> ASV7 1 90
#> ASV8 1 52
#> ASV12 1 630
#> ASV18 1 3
#> ASV25 1 1
#> Z29-001-H_S185_MERGED.fastq.gz Z30-ABM560-M_S187_MERGED.fastq.gz
#> ASV7 1 277
#> ASV8 1 9389
#> ASV12 1 1
#> ASV18 1 130
#> ASV25 1 1
#> 40 more rows ...
#>
#> $samples
#> group lib.size norm.factors
#> A10-005-B_S188_MERGED.fastq.gz Low 1930 0.32203429
#> A10-005-H_S189_MERGED.fastq.gz High 10246 0.06021446
#> A10-005-M_S190_MERGED.fastq.gz Middle 1179 0.52759695
#> A12-007-B_S2_MERGED.fastq.gz Low 1914 0.30630862
#> AB29-ABMX-H_S6_MERGED.fastq.gz High 1851 0.33312036
#> 85 more rows ...
#>
#> $genes
#> Domain Phylum Class Order Family
#> ASV7 Fungi Basidiomycota Agaricomycetes Russulales Stereaceae
#> ASV8 Fungi Basidiomycota Agaricomycetes Russulales Stereaceae
#> ASV12 Fungi Basidiomycota Agaricomycetes Hymenochaetales Schizoporaceae
#> ASV18 Fungi Basidiomycota Agaricomycetes Russulales Stereaceae
#> ASV25 Fungi Basidiomycota Agaricomycetes Agaricales Lyophyllaceae
#> Genus Species Trophic.Mode Guild
#> ASV7 <NA> <NA> Saprotroph Wood Saprotroph-Undefined Saprotroph
#> ASV8 Stereum ostrea Saprotroph Undefined Saprotroph
#> ASV12 Xylodon raduloides Saprotroph Undefined Saprotroph
#> ASV18 Stereum ostrea Saprotroph Undefined Saprotroph
#> ASV25 Ossicaulis lachnopus Saprotroph Wood Saprotroph
#> Trait Confidence.Ranking Genus_species
#> ASV7 NULL Probable NA_NA
#> ASV8 White Rot Probable Stereum_ostrea
#> ASV12 White Rot Probable Xylodon_raduloides
#> ASV18 White Rot Probable Stereum_ostrea
#> ASV25 Brown Rot Probable Ossicaulis_lachnopus
#> 40 more rows ...
#>
#> $common.dispersion
#> [1] 3.269437
#>
#> $pseudo.counts
#> A10-005-B_S188_MERGED.fastq.gz A10-005-H_S189_MERGED.fastq.gz
#> ASV7 739.9845140 9888.7370815
#> ASV8 557.8797556 9.7036208
#> ASV12 0.9605827 1.9385836
#> ASV18 29.8644385 0.9683215
#> ASV25 0.9603193 0.9678363
#> A10-005-M_S190_MERGED.fastq.gz A12-007-B_S2_MERGED.fastq.gz
#> ASV7 254.1481708 1.023169
#> ASV8 385.0731375 847.747007
#> ASV12 0.9594440 1.023116
#> ASV18 3.8464905 1063.167359
#> ASV25 0.9595064 1.023198
#> AB29-ABMX-H_S6_MERGED.fastq.gz AD26-005-B_S9_MERGED.fastq.gz
#> ASV7 0.9689209 1.023169
#> ASV8 1.9400514 1.023180
#> ASV12 1.9397400 1.023116
#> ASV18 0.9689180 1.023324
#> ASV25 0.9684418 1.023198
#> AD26-005-H_S10_MERGED.fastq.gz AD26-005-M_S11_MERGED.fastq.gz
#> ASV7 1.023085 1.9399666
#> ASV8 1.023087 0.9689068
#> ASV12 1.023234 1300.5607631
#> ASV18 1.023087 0.9684377
#> ASV25 1.023452 0.9687233
#> AD30-ABMX-M_S12_MERGED.fastq.gz AD32-007-M_S13_MERGED.fastq.gz
#> ASV7 1.025971 0.9682712
#> ASV8 2.050025 7.7623786
#> ASV12 1.026152 0.9680578
#> ASV18 1.026342 0.9678321
#> ASV25 1.026014 0.9681221
#> ADABM30X-B_S14_MERGED.fastq.gz ADABM30X-H_S15_MERGED.fastq.gz
#> ASV7 0.9604967 524.1303861
#> ASV8 2.8871709 2.9094842
#> ASV12 0.9605827 0.9681280
#> ASV18 0.9602419 0.9683215
#> ASV25 0.9603193 2.9086060
#> ADABM30X-M_S16_MERGED.fastq.gz B18-006-B_S19_MERGED.fastq.gz
#> ASV7 1.020353 1.028159
#> ASV8 1.020327 1.028173
#> ASV12 1.020494 1.028094
#> ASV18 1.020643 1.028348
#> ASV25 1.020393 1.028186
#> BA17-050-B_S21_MERGED.fastq.gz BB19-006-H_S22_MERGED.fastq.gz
#> ASV7 2800.3646390 1.020317
#> ASV8 4.8502866 9925.530722
#> ASV12 0.9682836 1.020448
#> ASV18 0.9680080 12189.387541
#> ASV25 0.9680837 1.020640
#> BB6-019-M_S25_MERGED.fastq.gz BG7-010-H_S31_MERGED.fastq.gz
#> ASV7 848.3304311 1.028057
#> ASV8 327.0949300 1.028059
#> ASV12 0.9680578 1.028238
#> ASV18 7.7614518 1.028059
#> ASV25 0.9681221 1.028504
#> BJ17-007-M_S34_MERGED.fastq.gz BL7-006-H_S37_MERGED.fastq.gz
#> ASV7 0.9513405 1.028057
#> ASV8 6.6806803 3.080174
#> ASV12 6.6795323 1.028238
#> ASV18 0.9506736 1.028059
#> ASV25 1.9092417 1.028504
#> BP11-001-B_S43_MERGED.fastq.gz BP11-001-H_S44_MERGED.fastq.gz
#> ASV7 1.023169 958.6644070
#> ASV8 2.044684 8.6682003
#> ASV12 2.044579 0.9603903
#> ASV18 1.023324 1778.5974801
#> ASV25 1.023198 0.9600293
#> BP11-001-M_S45_MERGED.fastq.gz BP12-025-B_S46_MERGED.fastq.gz
#> ASV7 6.7955611 1.028159
#> ASV8 6.7957113 2.054307
#> ASV12 0.9686592 1.028094
#> ASV18 0.9684377 1.028348
#> ASV25 0.9687233 1.028186
#> BQ4-018-B_S49_MERGED.fastq.gz BQ4-018-H_S50_MERGED.fastq.gz
#> ASV7 1.028159 1.023085
#> ASV8 2.054307 2.044529
#> ASV12 1.028094 1.023234
#> ASV18 1.028348 1.023087
#> ASV25 1.028186 2.045074
#> BQ4-018-M_S51_MERGED.fastq.gz BT-006-M_S55_MERGED.fastq.gz
#> ASV7 1.023126 1.025971
#> ASV8 1.023096 1.025938
#> ASV12 1.023287 1.026152
#> ASV18 1.023455 1.026342
#> ASV25 1.023168 1.026014
#> BV11-002-B_S57_MERGED.fastq.gz BV11-002-H_S58_MERGED.fastq.gz
#> ASV7 0.9688125 0.9689209
#> ASV8 3.8820095 2.9111887
#> ASV12 7333.4712076 0.9687281
#> ASV18 0.9686103 0.9689180
#> ASV25 0.9686856 65.0759416
#> BV11-002-M_S59_MERGED.fastq.gz C21-NV1-B_S62_MERGED.fastq.gz
#> ASV7 1.025971 1.023169
#> ASV8 1.025938 1.023180
#> ASV12 1.026152 1.023116
#> ASV18 1.026342 1.023324
#> ASV25 1.026014 1.023198
#> CB8-019-B_S69_MERGED.fastq.gz CB8-019-H_S70_MERGED.fastq.gz
#> ASV7 1.026019 1.025925
#> ASV8 1.026032 1.025928
#> ASV12 2.050063 1.026092
#> ASV18 1.026194 1.025928
#> ASV25 1.026048 1.026338
#> CB8-019-M_S71_MERGED.fastq.gz D18-003-B_S78_MERGED.fastq.gz
#> ASV7 1.025971 38.5348734
#> ASV8 1.025938 30.8270362
#> ASV12 3.074539 0.9605827
#> ASV18 1.026342 0.9602419
#> ASV25 1.026014 0.9603193
#> D18-003-M_S80_MERGED.fastq.gz D61-010-B_S82_MERGED.fastq.gz
#> ASV7 1.025971 0.9688125
#> ASV8 1.025938 5.8242097
#> ASV12 2.050366 1.9399871
#> ASV18 1.026342 0.9686103
#> ASV25 1.026014 4.8647768
#> D9-027-H_S84_MERGED.fastq.gz D9-027-M_S85_MERGED.fastq.gz
#> ASV7 1.028057 1.028106
#> ASV8 4.106226 2.054137
#> ASV12 1.028238 1.028302
#> ASV18 1.028059 1.028508
#> ASV25 1.028504 1.028149
#> DJ2-008-H_S88_MERGED.fastq.gz DS1-ABM002-B_S91_MERGED.fastq.gz
#> ASV7 1.020317 1.026019
#> ASV8 1.020319 1.026032
#> ASV12 1.020448 1.025960
#> ASV18 1.020319 1.026194
#> ASV25 1.020640 1.026048
#> DS1-ABM002-H_S92_MERGED.fastq.gz DS1-ABM002-M_S93_MERGED.fastq.gz
#> ASV7 0.9683244 0.9682712
#> ASV8 0.9683218 0.9683101
#> ASV12 0.9681280 0.9680578
#> ASV18 0.9683215 0.9678321
#> ASV25 1.9381709 3.8883517
#> DU3-045-B_S94_MERGED.fastq.gz DY5-004-B_S96_MERGED.fastq.gz
#> ASV7 32.7270259 1.023169
#> ASV8 1067.6859062 1.023180
#> ASV12 7.6981393 1.023116
#> ASV18 7.6971939 1.023324
#> ASV25 0.9594583 1.023198
#> DY5-004-H_S97_MERGED.fastq.gz EC2-013-B_S104_MERGED.fastq.gz
#> ASV7 1.025925 0.9688125
#> ASV8 1.025928 1.9398500
#> ASV12 1.026092 0.9688808
#> ASV18 1.025928 0.9686103
#> ASV25 1.026338 0.9686856
#> F7-015-M_S106_MERGED.fastq.gz FOMES19-H_S108_MERGED.fastq.gz
#> ASV7 1.025971 2.039187
#> ASV8 1.025938 1.020319
#> ASV12 1.026152 1.020448
#> ASV18 1.026342 1.020319
#> ASV25 1.026014 1.020640
#> FOMES19-M_S109_MERGED.fastq.gz H10-018-M_S110_MERGED.fastq.gz
#> ASV7 1.023126 1.028106
#> ASV8 1.023096 2.054137
#> ASV12 1.023287 1.028302
#> ASV18 1.023455 1.028508
#> ASV25 1.023168 1.028149
#> H24-NVABM1-H_S111_MERGED.fastq.gz J18-004-B_S114_MERGED.fastq.gz
#> ASV7 106.981018 1.026019
#> ASV8 1.020319 1.026032
#> ASV12 3.058330 1.025960
#> ASV18 1.020319 1.026194
#> ASV25 10.190628 2.048230
#> J18-004-M_S116_MERGED.fastq.gz K18-002-H_S117_MERGED.fastq.gz
#> ASV7 1.028106 34.9592516
#> ASV8 1.028070 0.9689183
#> ASV12 1.028302 0.9687281
#> ASV18 1.028508 33.0169042
#> ASV25 1.028149 0.9684418
#> L19X-B_S119_MERGED.fastq.gz L19X-H_S120_MERGED.fastq.gz
#> ASV7 1.026019 326.1238049
#> ASV8 187.400182 35.9098544
#> ASV12 1.025960 0.9681280
#> ASV18 1.026194 9.7036189
#> ASV25 1.026048 0.9678363
#> L19X-M_S121_MERGED.fastq.gz L23-002-B_S122_MERGED.fastq.gz
#> ASV7 2698.7914099 6.7407990
#> ASV8 428.7466466 32.7539900
#> ASV12 0.9603035 0.9605827
#> ASV18 21.1940575 26.9737587
#> ASV25 0.9603664 0.9603193
#> L23-002-H_S123_MERGED.fastq.gz L23-002-M_S124_MERGED.fastq.gz
#> ASV7 1949.4596380 1.023126
#> ASV8 2032.2538022 155.257416
#> ASV12 0.9595327 1.023287
#> ASV18 100.1154865 38.812658
#> ASV25 0.9591640 1.023168
#> N19X-H_S127_MERGED.fastq.gz N19X-M_S128_MERGED.fastq.gz
#> ASV7 1440.3991066 166.9431303
#> ASV8 2249.9023873 273.7107127
#> ASV12 0.9681280 0.9680578
#> ASV18 162.0894130 11.6441341
#> ASV25 0.9678363 0.9681221
#> N23-002-B_S130_MERGED.fastq.gz N23-002-H_S131_MERGED.fastq.gz
#> ASV7 1.026019 1.023085
#> ASV8 1.026032 2.044529
#> ASV12 1.025960 1.023234
#> ASV18 1.026194 1.023087
#> ASV25 1.026048 446.265835
#> NVABM-0163-H_S135_MERGED.fastq.gz NVABM0244-M_S137_MERGED.fastq.gz
#> ASV7 1.025925 1.025971
#> ASV8 1.025928 1.025938
#> ASV12 1.026092 1.026152
#> ASV18 1.025928 1.026342
#> ASV25 1.026338 1.026014
#> O20-X-H_S140_MERGED.fastq.gz O20-X-M_S141_MERGED.fastq.gz
#> ASV7 98.190154 2049.0165024
#> ASV8 22.138363 857.0565881
#> ASV12 1520.257340 3.8794388
#> ASV18 3.847720 67.9518495
#> ASV25 0.959164 0.9681221
#> O24-003-B_S145_MERGED.fastq.gz O26-004-B_S148_MERGED.fastq.gz
#> ASV7 1.028159 1.023169
#> ASV8 3.080422 1.023180
#> ASV12 1.028094 1.023116
#> ASV18 1.028348 1.023324
#> ASV25 1.028186 1.023198
#> O9-005-B_S152_MERGED.fastq.gz P19-023-M_S153_MERGED.fastq.gz
#> ASV7 0.9682140 2.044594
#> ASV8 1.9386956 27.580317
#> ASV12 1.9388353 1.023287
#> ASV18 0.9680080 1.023455
#> ASV25 0.9680837 1.023168
#> P27-015-M_S154_MERGED.fastq.gz Q27-ABM003-B_S156_MERGED.fastq.gz
#> ASV7 1.020353 1.026019
#> ASV8 196.639498 483.338087
#> ASV12 8.152919 1.025960
#> ASV18 282.172711 1.026194
#> ASV25 1.020393 1.026048
#> T28-ABM602-B_S162_MERGED.fastq.gz W26-001-B_S165_MERGED.fastq.gz
#> ASV7 1.023169 1.028159
#> ASV8 1.023180 1.028173
#> ASV12 1.023116 1.028094
#> ASV18 1.023324 1.028348
#> ASV25 1.023198 1.028186
#> W9-025-M_S169_MERGED.fastq.gz X24-009-B_S170_MERGED.fastq.gz
#> ASV7 1.028106 0.9688125
#> ASV8 1.028070 0.9687977
#> ASV12 1.028302 0.9688808
#> ASV18 1.028508 0.9686103
#> ASV25 1.028149 0.9686856
#> X24-009-H_S171_MERGED.fastq.gz X24-009-M_S172_MERGED.fastq.gz
#> ASV7 1.9389054 0.9605674
#> ASV8 5.8212488 7.7046802
#> ASV12 0.9681280 0.9603035
#> ASV18 0.9683215 0.9600240
#> ASV25 0.9678363 0.9603664
#> X29-004-B_S174_MERGED.fastq.gz X29-004-H_S175_MERGED.fastq.gz
#> ASV7 1.028159 104.0517756
#> ASV8 1.028173 108.8691295
#> ASV12 1.028094 0.9603903
#> ASV18 1.028348 1.9240643
#> ASV25 1.028186 0.9600293
#> X29-004-M_S176_MERGED.fastq.gz Y21-ABM484-H_S177_MERGED.fastq.gz
#> ASV7 1.023126 1.020317
#> ASV8 3.065988 2.039190
#> ASV12 1.023287 254.704323
#> ASV18 1.023455 1.020319
#> ASV25 1.023168 1.020640
#> Y28-002-B_S178_MERGED.fastq.gz Y31-ABM484-B_S184_MERGED.fastq.gz
#> ASV7 1.028159 86.6383224
#> ASV8 1.028173 50.0555269
#> ASV12 1.028094 606.4994165
#> ASV18 1.028348 2.8842769
#> ASV25 1.028186 0.9594583
#> Z29-001-H_S185_MERGED.fastq.gz Z30-ABM560-M_S187_MERGED.fastq.gz
#> ASV7 1.028057 269.0126340
#> ASV8 1.028059 9118.4411470
#> ASV12 1.028238 0.9686592
#> ASV18 1.028059 126.2769656
#> ASV25 1.028504 0.9687233
#> 40 more rows ...
#>
#> $pseudo.lib.size
#> [1] 598.8289
#>
#> $AveLogCPM
#> [1] 18.85258 19.06397 17.66999 18.18946 13.84983
#> 40 more elements ...
#>
#> $prior.df
#> [1] 10
#>
#> $prior.n
#> [1] 0.1149425
#>
#> $tagwise.dispersion
#> [1] 5.655012 5.359018 5.694498 4.969208 1.650035
#> 40 more elements ...
#>
#> $span
#> [1] 0.3
#>
# }