Compute and test local contributions to beta diversity (LCBD) of samples
Source:R/beta_div_test.R
LCBD_pq.Rd
A wrapper for the adespatial::beta.div() function in the case of physeq
object.
Arguments
- physeq
(required): a
phyloseq-classobject obtained using thephyloseqpackage.- p_adjust_method
(chr, default "BH"): the method used to adjust p-value
- ...
Other arguments passed on to
adespatial::beta.div()function
Value
An object of class beta.div see adespatial::beta.div() function
for more information
Author
Adrien Taudière
This function is mainly a wrapper of the work of others.
Please make a reference to adespatial::beta.div() if you
use this function.
Examples
if (requireNamespace("adespatial")) {
res <- LCBD_pq(data_fungi_sp_known, nperm = 5)
str(res)
length(res$LCBD)
length(res$SCBD)
}
#> List of 8
#> $ beta : Named num [1:2] 173.703 0.944
#> ..- attr(*, "names")= chr [1:2] "SStotal" "BDtotal"
#> $ SCBD : Named num [1:651] 0.0533 0.0307 0.0206 0.0123 0.0122 ...
#> ..- attr(*, "names")= chr [1:651] "ASV2" "ASV8" "ASV12" "ASV18" ...
#> $ LCBD : Named num [1:185] 0.00522 0.00559 0.00545 0.00516 0.00488 ...
#> ..- attr(*, "names")= chr [1:185] "A10-005-B_S188_MERGED.fastq.gz" "A10-005-H_S189_MERGED.fastq.gz" "A10-005-M_S190_MERGED.fastq.gz" "A12-007_S191_MERGED.fastq.gz" ...
#> $ p.LCBD: Named num [1:185] 0.833 0.5 0.5 1 1 ...
#> ..- attr(*, "names")= chr [1:185] "A10-005-B_S188_MERGED.fastq.gz" "A10-005-H_S189_MERGED.fastq.gz" "A10-005-M_S190_MERGED.fastq.gz" "A12-007_S191_MERGED.fastq.gz" ...
#> $ p.adj : Named num [1:185] 1 0.898 0.898 1 1 ...
#> ..- attr(*, "names")= chr [1:185] "A10-005-B_S188_MERGED.fastq.gz" "A10-005-H_S189_MERGED.fastq.gz" "A10-005-M_S190_MERGED.fastq.gz" "A12-007_S191_MERGED.fastq.gz" ...
#> $ method: chr [1:2] "hellinger" NA
#> $ note : chr "Info -- This coefficient is Euclidean"
#> $ D : logi NA
#> - attr(*, "class")= chr "beta.div"
#> [1] 651
# \donttest{
if (requireNamespace("adespatial")) {
LCBD_pq(data_fungi_sp_known, nperm = 5, method = "jaccard")
}
#> $beta
#> SStotal BDtotal
#> 86.5283720 0.4702629
#>
#> $SCBD
#> [1] NA
#>
#> $LCBD
#> A10-005-B_S188_MERGED.fastq.gz A10-005-H_S189_MERGED.fastq.gz
#> 0.005398284 0.005550668
#> A10-005-M_S190_MERGED.fastq.gz A12-007_S191_MERGED.fastq.gz
#> 0.005444845 0.005441464
#> A12-007-B_S2_MERGED.fastq.gz A15-004_S3_MERGED.fastq.gz
#> 0.005461737 0.005078194
#> A8-005_S4_MERGED.fastq.gz A9-012_S5_MERGED.fastq.gz
#> 0.005360522 0.005128489
#> AB29-ABMX-H_S6_MERGED.fastq.gz AC27-013_S7_MERGED.fastq.gz
#> 0.005563478 0.005330179
#> AC29033_S8_MERGED.fastq.gz AD26-005-B_S9_MERGED.fastq.gz
#> 0.005402056 0.005555455
#> AD26-005-H_S10_MERGED.fastq.gz AD26-005-M_S11_MERGED.fastq.gz
#> 0.005506894 0.005566377
#> AD30-ABMX-M_S12_MERGED.fastq.gz AD32-007-M_S13_MERGED.fastq.gz
#> 0.005466833 0.005382835
#> ADABM30X-B_S14_MERGED.fastq.gz ADABM30X-H_S15_MERGED.fastq.gz
#> 0.005487170 0.005481407
#> ADABM30X-M_S16_MERGED.fastq.gz AE30-ABM507_S17_MERGED.fastq.gz
#> 0.005628821 0.005384814
#> B17-014_S18_MERGED.fastq.gz B18-006-B_S19_MERGED.fastq.gz
#> 0.005192392 0.005094756
#> BA16-036bis_S20_MERGED.fastq.gz BA17-050-B_S21_MERGED.fastq.gz
#> 0.005561127 0.005350902
#> BB19-006-H_S22_MERGED.fastq.gz BB6-019-B_S23_MERGED.fastq.gz
#> 0.005446338 0.005439750
#> BB6-019-H_S24_MERGED.fastq.gz BB6-019-M_S25_MERGED.fastq.gz
#> 0.005482589 0.005373188
#> BD14-021_S26_MERGED.fastq.gz BE9-006-B_S27_MERGED.fastq.gz
#> 0.005358611 0.005383989
#> BE9-006-H_S28_MERGED.fastq.gz BE9-006-M_S29_MERGED.fastq.gz
#> 0.005355821 0.005395364
#> BG7-010-B_S30_MERGED.fastq.gz BG7-010-H_S31_MERGED.fastq.gz
#> 0.004943752 0.005220289
#> BG7-010-M_S32_MERGED.fastq.gz BH9-021_S33_MERGED.fastq.gz
#> 0.004970198 0.005257841
#> BJ17-007-M_S34_MERGED.fastq.gz BJ8-ABM-003_S35_MERGED.fastq.gz
#> 0.005377047 0.005577087
#> BL7-006-B_S36_MERGED.fastq.gz BL7-006-H_S37_MERGED.fastq.gz
#> 0.004999042 0.004963713
#> BL7-006-M_S38_MERGED.fastq.gz BN11-041_S39_MERGED.fastq.gz
#> 0.004781180 0.005429140
#> BN9-002_S40_MERGED.fastq.gz BO8-002_S41_MERGED.fastq.gz
#> 0.005665252 0.005517642
#> BO8-005_S42_MERGED.fastq.gz BP11-001-B_S43_MERGED.fastq.gz
#> 0.005573845 0.005494164
#> BP11-001-H_S44_MERGED.fastq.gz BP11-001-M_S45_MERGED.fastq.gz
#> 0.005338535 0.005495800
#> BP12-025-B_S46_MERGED.fastq.gz BP14-006_S47_MERGED.fastq.gz
#> 0.005556655 0.005326438
#> BQ3-019_S48_MERGED.fastq.gz BQ4-018-B_S49_MERGED.fastq.gz
#> 0.005665118 0.005356941
#> BQ4-018-H_S50_MERGED.fastq.gz BQ4-018-M_S51_MERGED.fastq.gz
#> 0.005491212 0.005571424
#> BQ9ABM-002_S52_MERGED.fastq.gz BR8-005_S53_MERGED.fastq.gz
#> 0.005497845 0.005491499
#> BS14-006_S54_MERGED.fastq.gz BT-006-M_S55_MERGED.fastq.gz
#> 0.005384537 0.005168301
#> BT7-006_S56_MERGED.fastq.gz BV11-002-B_S57_MERGED.fastq.gz
#> 0.005084315 0.005458463
#> BV11-002-H_S58_MERGED.fastq.gz BV11-002-M_S59_MERGED.fastq.gz
#> 0.005438616 0.005596859
#> BW8-003_S60_MERGED.fastq.gz C1-001_S61_MERGED.fastq.gz
#> 0.005346791 0.005276780
#> C21-NV1-B_S62_MERGED.fastq.gz C21-NV1-H_S63_MERGED.fastq.gz
#> 0.005511602 0.005477861
#> C21-NV1-M_S64_MERGED.fastq.gz C9-005_S65_MERGED.fastq.gz
#> 0.005707347 0.005590082
#> CA12-024_S66_MERGED.fastq.gz CA9-027_S67_MERGED.fastq.gz
#> 0.005552383 0.005706414
#> CA9-X_S68_MERGED.fastq.gz CB8-019-B_S69_MERGED.fastq.gz
#> 0.005426847 0.005571891
#> CB8-019-H_S70_MERGED.fastq.gz CB8-019-M_S71_MERGED.fastq.gz
#> 0.005502441 0.005530143
#> CB9-013_S72_MERGED.fastq.gz CC3-044_S73_MERGED.fastq.gz
#> 0.005490287 0.005457918
#> CC8-003_S74_MERGED.fastq.gz D17-011_S77_MERGED.fastq.gz
#> 0.005601528 0.005358224
#> D18-003-B_S78_MERGED.fastq.gz D18-003-H_S79_MERGED.fastq.gz
#> 0.005457737 0.005522691
#> D18-003-M_S80_MERGED.fastq.gz D22-NVABM1_S81_MERGED.fastq.gz
#> 0.005577862 0.005366414
#> D61-010-B_S82_MERGED.fastq.gz D9-027-B_S83_MERGED.fastq.gz
#> 0.005491082 0.005212816
#> D9-027-H_S84_MERGED.fastq.gz D9-027-M_S85_MERGED.fastq.gz
#> 0.005028374 0.005239751
#> DBM-ABM-001_S86_MERGED.fastq.gz DJ2-008-B_S87_MERGED.fastq.gz
#> 0.005312083 0.005399521
#> DJ2-008-H_S88_MERGED.fastq.gz DJ2-008-M_S89_MERGED.fastq.gz
#> 0.005631249 0.005280451
#> DP4-ABM001_S90_MERGED.fastq.gz DS1-ABM002-B_S91_MERGED.fastq.gz
#> 0.005565384 0.005478764
#> DS1-ABM002-H_S92_MERGED.fastq.gz DS1-ABM002-M_S93_MERGED.fastq.gz
#> 0.005653426 0.005492775
#> DU3-045-B_S94_MERGED.fastq.gz DW4-007_S95_MERGED.fastq.gz
#> 0.005348383 0.005466873
#> DY5-004-B_S96_MERGED.fastq.gz DY5-004-H_S97_MERGED.fastq.gz
#> 0.005152746 0.005059661
#> DY5-004-M_S98_MERGED.fastq.gz DZ6-ABM-001_S99_MERGED.fastq.gz
#> 0.005173344 0.005558530
#> E9-009-B_S100_MERGED.fastq.gz E9-009-H_S101_MERGED.fastq.gz
#> 0.005064167 0.005023463
#> E9-009-M_S102_MERGED.fastq.gz EA5-ABM-001_S103_MERGED.fastq.gz
#> 0.004953764 0.005481721
#> EC2-013-B_S104_MERGED.fastq.gz F6-ABM-001_S105_MERGED.fastq.gz
#> 0.005547660 0.005730904
#> F7-015-M_S106_MERGED.fastq.gz FOMES19-H_S108_MERGED.fastq.gz
#> 0.005720220 0.005089936
#> FOMES19-M_S109_MERGED.fastq.gz H10-018-M_S110_MERGED.fastq.gz
#> 0.005206987 0.005538178
#> H24-NVABM1-H_S111_MERGED.fastq.gz J18-004-B_S114_MERGED.fastq.gz
#> 0.005239803 0.005151929
#> J18-004-H_S115_MERGED.fastq.gz J18-004-M_S116_MERGED.fastq.gz
#> 0.005762547 0.005134888
#> K18-002-H_S117_MERGED.fastq.gz K26-NVABM1_S118_MERGED.fastq.gz
#> 0.005491317 0.005502090
#> L19X-B_S119_MERGED.fastq.gz L19X-H_S120_MERGED.fastq.gz
#> 0.005739303 0.005516046
#> L19X-M_S121_MERGED.fastq.gz L23-002-B_S122_MERGED.fastq.gz
#> 0.005365199 0.005143392
#> L23-002-H_S123_MERGED.fastq.gz L23-002-M_S124_MERGED.fastq.gz
#> 0.005572630 0.005257109
#> M22-001_S125_MERGED.fastq.gz N19X-B_S126_MERGED.fastq.gz
#> 0.005584895 0.005041025
#> N19X-H_S127_MERGED.fastq.gz N19X-M_S128_MERGED.fastq.gz
#> 0.005264857 0.005377916
#> N22-001-B_S129_MERGED.fastq.gz N23-002-B_S130_MERGED.fastq.gz
#> 0.005760180 0.005470941
#> N23-002-H_S131_MERGED.fastq.gz N23-002-M_S132_MERGED.fastq.gz
#> 0.005471282 0.006089028
#> N25-ABMX_S133_MERGED.fastq.gz NVABM-0058_S134_MERGED.fastq.gz
#> 0.005535886 0.005464185
#> NVABM-0163-H_S135_MERGED.fastq.gz NVABM-0397_S138_MERGED.fastq.gz
#> 0.005517807 0.005507368
#> NVABM0216_S136_MERGED.fastq.gz NVABM0244-M_S137_MERGED.fastq.gz
#> 0.005634269 0.005716539
#> O20-X-B_S139_MERGED.fastq.gz O20-X-H_S140_MERGED.fastq.gz
#> 0.005550458 0.005216059
#> O20-X-M_S141_MERGED.fastq.gz O21-007-B_S142_MERGED.fastq.gz
#> 0.005206341 0.005466052
#> O21-007-H_S143_MERGED.fastq.gz O21-007-M_S144_MERGED.fastq.gz
#> 0.005573792 0.005933239
#> O24-003-B_S145_MERGED.fastq.gz O24-003-H_S146_MERGED.fastq.gz
#> 0.005314380 0.005468160
#> O24-003-M_S147_MERGED.fastq.gz O26-004-B_S148_MERGED.fastq.gz
#> 0.005296319 0.005563424
#> O26-004-H_S149_MERGED.fastq.gz O26-004-M_S150_MERGED.fastq.gz
#> 0.005538888 0.005737268
#> O27-012_S151_MERGED.fastq.gz O9-005-B_S152_MERGED.fastq.gz
#> 0.005585947 0.005091717
#> P19-023-M_S153_MERGED.fastq.gz P27-015-M_S154_MERGED.fastq.gz
#> 0.005550866 0.005619124
#> P27-ABM001_S155_MERGED.fastq.gz Q27-ABM003-B_S156_MERGED.fastq.gz
#> 0.005636609 0.005457268
#> R25-ABMX_S157_MERGED.fastq.gz R28-008-B_S158_MERGED.fastq.gz
#> 0.005415096 0.005101819
#> R28-008-H_S159_MERGED.fastq.gz R28-008-M_S160_MERGED.fastq.gz
#> 0.004987584 0.005077265
#> T28-011_S161_MERGED.fastq.gz T28-ABM602-B_S162_MERGED.fastq.gz
#> 0.005478888 0.005776477
#> U27-ABM002_S163_MERGED.fastq.gz W25-ABMX_S164_MERGED.fastq.gz
#> 0.005370920 0.005453257
#> W26-001-B_S165_MERGED.fastq.gz W26-001-H_S166_MERGED.fastq.gz
#> 0.004758101 0.004908588
#> W26-001-M_S167_MERGED.fastq.gz W30-006_S168_MERGED.fastq.gz
#> 0.005065333 0.005394839
#> W9-025-M_S169_MERGED.fastq.gz X24-009-B_S170_MERGED.fastq.gz
#> 0.005728282 0.005267850
#> X24-009-H_S171_MERGED.fastq.gz X24-009-M_S172_MERGED.fastq.gz
#> 0.005586239 0.005548480
#> X24-010_S173_MERGED.fastq.gz X29-004-B_S174_MERGED.fastq.gz
#> 0.005564110 0.005657518
#> X29-004-H_S175_MERGED.fastq.gz X29-004-M_S176_MERGED.fastq.gz
#> 0.005273738 0.005466336
#> Y21-ABM484-H_S177_MERGED.fastq.gz Y28-002-B_S178_MERGED.fastq.gz
#> 0.005373932 0.005279263
#> Y28-002-H_S179_MERGED.fastq.gz Y28-002-M_S180_MERGED.fastq.gz
#> 0.005125520 0.005339353
#> Y29-007-B_S181_MERGED.fastq.gz Y29-007-H_S182_MERGED.fastq.gz
#> 0.005127480 0.005094909
#> Y29-007-M_S183_MERGED.fastq.gz Y31-ABM484-B_S184_MERGED.fastq.gz
#> 0.005505642 0.005582052
#> Z29-001-H_S185_MERGED.fastq.gz Z30-002_S186_MERGED.fastq.gz
#> 0.005431650 0.005088953
#> Z30-ABM560-M_S187_MERGED.fastq.gz
#> 0.005368628
#>
#> $p.LCBD
#> A10-005-B_S188_MERGED.fastq.gz A10-005-H_S189_MERGED.fastq.gz
#> 0.6666667 0.3333333
#> A10-005-M_S190_MERGED.fastq.gz A12-007_S191_MERGED.fastq.gz
#> 0.6666667 0.5000000
#> A12-007-B_S2_MERGED.fastq.gz A15-004_S3_MERGED.fastq.gz
#> 0.3333333 1.0000000
#> A8-005_S4_MERGED.fastq.gz A9-012_S5_MERGED.fastq.gz
#> 0.6666667 1.0000000
#> AB29-ABMX-H_S6_MERGED.fastq.gz AC27-013_S7_MERGED.fastq.gz
#> 0.3333333 1.0000000
#> AC29033_S8_MERGED.fastq.gz AD26-005-B_S9_MERGED.fastq.gz
#> 0.6666667 0.1666667
#> AD26-005-H_S10_MERGED.fastq.gz AD26-005-M_S11_MERGED.fastq.gz
#> 0.1666667 0.1666667
#> AD30-ABMX-M_S12_MERGED.fastq.gz AD32-007-M_S13_MERGED.fastq.gz
#> 0.6666667 0.5000000
#> ADABM30X-B_S14_MERGED.fastq.gz ADABM30X-H_S15_MERGED.fastq.gz
#> 0.5000000 0.5000000
#> ADABM30X-M_S16_MERGED.fastq.gz AE30-ABM507_S17_MERGED.fastq.gz
#> 0.3333333 0.8333333
#> B17-014_S18_MERGED.fastq.gz B18-006-B_S19_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> BA16-036bis_S20_MERGED.fastq.gz BA17-050-B_S21_MERGED.fastq.gz
#> 0.3333333 0.3333333
#> BB19-006-H_S22_MERGED.fastq.gz BB6-019-B_S23_MERGED.fastq.gz
#> 0.3333333 0.8333333
#> BB6-019-H_S24_MERGED.fastq.gz BB6-019-M_S25_MERGED.fastq.gz
#> 0.3333333 0.6666667
#> BD14-021_S26_MERGED.fastq.gz BE9-006-B_S27_MERGED.fastq.gz
#> 0.5000000 0.3333333
#> BE9-006-H_S28_MERGED.fastq.gz BE9-006-M_S29_MERGED.fastq.gz
#> 0.6666667 0.5000000
#> BG7-010-B_S30_MERGED.fastq.gz BG7-010-H_S31_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> BG7-010-M_S32_MERGED.fastq.gz BH9-021_S33_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> BJ17-007-M_S34_MERGED.fastq.gz BJ8-ABM-003_S35_MERGED.fastq.gz
#> 1.0000000 0.1666667
#> BL7-006-B_S36_MERGED.fastq.gz BL7-006-H_S37_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> BL7-006-M_S38_MERGED.fastq.gz BN11-041_S39_MERGED.fastq.gz
#> 1.0000000 0.5000000
#> BN9-002_S40_MERGED.fastq.gz BO8-002_S41_MERGED.fastq.gz
#> 0.1666667 0.1666667
#> BO8-005_S42_MERGED.fastq.gz BP11-001-B_S43_MERGED.fastq.gz
#> 0.1666667 0.1666667
#> BP11-001-H_S44_MERGED.fastq.gz BP11-001-M_S45_MERGED.fastq.gz
#> 0.6666667 0.3333333
#> BP12-025-B_S46_MERGED.fastq.gz BP14-006_S47_MERGED.fastq.gz
#> 0.1666667 0.8333333
#> BQ3-019_S48_MERGED.fastq.gz BQ4-018-B_S49_MERGED.fastq.gz
#> 0.3333333 0.6666667
#> BQ4-018-H_S50_MERGED.fastq.gz BQ4-018-M_S51_MERGED.fastq.gz
#> 0.5000000 0.1666667
#> BQ9ABM-002_S52_MERGED.fastq.gz BR8-005_S53_MERGED.fastq.gz
#> 0.5000000 0.1666667
#> BS14-006_S54_MERGED.fastq.gz BT-006-M_S55_MERGED.fastq.gz
#> 0.8333333 1.0000000
#> BT7-006_S56_MERGED.fastq.gz BV11-002-B_S57_MERGED.fastq.gz
#> 1.0000000 0.3333333
#> BV11-002-H_S58_MERGED.fastq.gz BV11-002-M_S59_MERGED.fastq.gz
#> 0.6666667 0.1666667
#> BW8-003_S60_MERGED.fastq.gz C1-001_S61_MERGED.fastq.gz
#> 0.6666667 0.8333333
#> C21-NV1-B_S62_MERGED.fastq.gz C21-NV1-H_S63_MERGED.fastq.gz
#> 0.1666667 0.1666667
#> C21-NV1-M_S64_MERGED.fastq.gz C9-005_S65_MERGED.fastq.gz
#> 0.1666667 0.1666667
#> CA12-024_S66_MERGED.fastq.gz CA9-027_S67_MERGED.fastq.gz
#> 0.3333333 0.1666667
#> CA9-X_S68_MERGED.fastq.gz CB8-019-B_S69_MERGED.fastq.gz
#> 0.5000000 0.1666667
#> CB8-019-H_S70_MERGED.fastq.gz CB8-019-M_S71_MERGED.fastq.gz
#> 0.5000000 0.1666667
#> CB9-013_S72_MERGED.fastq.gz CC3-044_S73_MERGED.fastq.gz
#> 0.3333333 0.3333333
#> CC8-003_S74_MERGED.fastq.gz D17-011_S77_MERGED.fastq.gz
#> 0.1666667 0.5000000
#> D18-003-B_S78_MERGED.fastq.gz D18-003-H_S79_MERGED.fastq.gz
#> 0.1666667 0.6666667
#> D18-003-M_S80_MERGED.fastq.gz D22-NVABM1_S81_MERGED.fastq.gz
#> 0.1666667 0.3333333
#> D61-010-B_S82_MERGED.fastq.gz D9-027-B_S83_MERGED.fastq.gz
#> 0.5000000 1.0000000
#> D9-027-H_S84_MERGED.fastq.gz D9-027-M_S85_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> DBM-ABM-001_S86_MERGED.fastq.gz DJ2-008-B_S87_MERGED.fastq.gz
#> 1.0000000 0.5000000
#> DJ2-008-H_S88_MERGED.fastq.gz DJ2-008-M_S89_MERGED.fastq.gz
#> 0.5000000 1.0000000
#> DP4-ABM001_S90_MERGED.fastq.gz DS1-ABM002-B_S91_MERGED.fastq.gz
#> 0.1666667 0.5000000
#> DS1-ABM002-H_S92_MERGED.fastq.gz DS1-ABM002-M_S93_MERGED.fastq.gz
#> 0.1666667 0.1666667
#> DU3-045-B_S94_MERGED.fastq.gz DW4-007_S95_MERGED.fastq.gz
#> 1.0000000 0.8333333
#> DY5-004-B_S96_MERGED.fastq.gz DY5-004-H_S97_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> DY5-004-M_S98_MERGED.fastq.gz DZ6-ABM-001_S99_MERGED.fastq.gz
#> 1.0000000 0.1666667
#> E9-009-B_S100_MERGED.fastq.gz E9-009-H_S101_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> E9-009-M_S102_MERGED.fastq.gz EA5-ABM-001_S103_MERGED.fastq.gz
#> 1.0000000 0.1666667
#> EC2-013-B_S104_MERGED.fastq.gz F6-ABM-001_S105_MERGED.fastq.gz
#> 0.1666667 0.1666667
#> F7-015-M_S106_MERGED.fastq.gz FOMES19-H_S108_MERGED.fastq.gz
#> 0.1666667 1.0000000
#> FOMES19-M_S109_MERGED.fastq.gz H10-018-M_S110_MERGED.fastq.gz
#> 0.8333333 0.1666667
#> H24-NVABM1-H_S111_MERGED.fastq.gz J18-004-B_S114_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> J18-004-H_S115_MERGED.fastq.gz J18-004-M_S116_MERGED.fastq.gz
#> 0.1666667 1.0000000
#> K18-002-H_S117_MERGED.fastq.gz K26-NVABM1_S118_MERGED.fastq.gz
#> 0.3333333 0.1666667
#> L19X-B_S119_MERGED.fastq.gz L19X-H_S120_MERGED.fastq.gz
#> 0.1666667 0.1666667
#> L19X-M_S121_MERGED.fastq.gz L23-002-B_S122_MERGED.fastq.gz
#> 0.6666667 0.8333333
#> L23-002-H_S123_MERGED.fastq.gz L23-002-M_S124_MERGED.fastq.gz
#> 0.3333333 1.0000000
#> M22-001_S125_MERGED.fastq.gz N19X-B_S126_MERGED.fastq.gz
#> 0.1666667 1.0000000
#> N19X-H_S127_MERGED.fastq.gz N19X-M_S128_MERGED.fastq.gz
#> 1.0000000 0.5000000
#> N22-001-B_S129_MERGED.fastq.gz N23-002-B_S130_MERGED.fastq.gz
#> 0.1666667 0.1666667
#> N23-002-H_S131_MERGED.fastq.gz N23-002-M_S132_MERGED.fastq.gz
#> 0.3333333 0.1666667
#> N25-ABMX_S133_MERGED.fastq.gz NVABM-0058_S134_MERGED.fastq.gz
#> 0.3333333 0.3333333
#> NVABM-0163-H_S135_MERGED.fastq.gz NVABM-0397_S138_MERGED.fastq.gz
#> 0.1666667 0.1666667
#> NVABM0216_S136_MERGED.fastq.gz NVABM0244-M_S137_MERGED.fastq.gz
#> 0.3333333 0.1666667
#> O20-X-B_S139_MERGED.fastq.gz O20-X-H_S140_MERGED.fastq.gz
#> 0.1666667 1.0000000
#> O20-X-M_S141_MERGED.fastq.gz O21-007-B_S142_MERGED.fastq.gz
#> 1.0000000 0.8333333
#> O21-007-H_S143_MERGED.fastq.gz O21-007-M_S144_MERGED.fastq.gz
#> 0.3333333 0.1666667
#> O24-003-B_S145_MERGED.fastq.gz O24-003-H_S146_MERGED.fastq.gz
#> 1.0000000 0.1666667
#> O24-003-M_S147_MERGED.fastq.gz O26-004-B_S148_MERGED.fastq.gz
#> 0.8333333 0.3333333
#> O26-004-H_S149_MERGED.fastq.gz O26-004-M_S150_MERGED.fastq.gz
#> 0.1666667 0.1666667
#> O27-012_S151_MERGED.fastq.gz O9-005-B_S152_MERGED.fastq.gz
#> 0.1666667 1.0000000
#> P19-023-M_S153_MERGED.fastq.gz P27-015-M_S154_MERGED.fastq.gz
#> 0.1666667 0.1666667
#> P27-ABM001_S155_MERGED.fastq.gz Q27-ABM003-B_S156_MERGED.fastq.gz
#> 0.3333333 0.3333333
#> R25-ABMX_S157_MERGED.fastq.gz R28-008-B_S158_MERGED.fastq.gz
#> 0.5000000 1.0000000
#> R28-008-H_S159_MERGED.fastq.gz R28-008-M_S160_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> T28-011_S161_MERGED.fastq.gz T28-ABM602-B_S162_MERGED.fastq.gz
#> 0.1666667 0.1666667
#> U27-ABM002_S163_MERGED.fastq.gz W25-ABMX_S164_MERGED.fastq.gz
#> 0.6666667 0.8333333
#> W26-001-B_S165_MERGED.fastq.gz W26-001-H_S166_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> W26-001-M_S167_MERGED.fastq.gz W30-006_S168_MERGED.fastq.gz
#> 1.0000000 0.5000000
#> W9-025-M_S169_MERGED.fastq.gz X24-009-B_S170_MERGED.fastq.gz
#> 0.1666667 1.0000000
#> X24-009-H_S171_MERGED.fastq.gz X24-009-M_S172_MERGED.fastq.gz
#> 0.1666667 0.1666667
#> X24-010_S173_MERGED.fastq.gz X29-004-B_S174_MERGED.fastq.gz
#> 0.5000000 0.1666667
#> X29-004-H_S175_MERGED.fastq.gz X29-004-M_S176_MERGED.fastq.gz
#> 1.0000000 0.3333333
#> Y21-ABM484-H_S177_MERGED.fastq.gz Y28-002-B_S178_MERGED.fastq.gz
#> 0.8333333 0.8333333
#> Y28-002-H_S179_MERGED.fastq.gz Y28-002-M_S180_MERGED.fastq.gz
#> 1.0000000 0.8333333
#> Y29-007-B_S181_MERGED.fastq.gz Y29-007-H_S182_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> Y29-007-M_S183_MERGED.fastq.gz Y31-ABM484-B_S184_MERGED.fastq.gz
#> 0.3333333 0.3333333
#> Z29-001-H_S185_MERGED.fastq.gz Z30-002_S186_MERGED.fastq.gz
#> 0.5000000 1.0000000
#> Z30-ABM560-M_S187_MERGED.fastq.gz
#> 0.8333333
#>
#> $p.adj
#> A10-005-B_S188_MERGED.fastq.gz A10-005-H_S189_MERGED.fastq.gz
#> 1.0000000 0.7254902
#> A10-005-M_S190_MERGED.fastq.gz A12-007_S191_MERGED.fastq.gz
#> 1.0000000 0.8726415
#> A12-007-B_S2_MERGED.fastq.gz A15-004_S3_MERGED.fastq.gz
#> 0.7254902 1.0000000
#> A8-005_S4_MERGED.fastq.gz A9-012_S5_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> AB29-ABMX-H_S6_MERGED.fastq.gz AC27-013_S7_MERGED.fastq.gz
#> 0.7254902 1.0000000
#> AC29033_S8_MERGED.fastq.gz AD26-005-B_S9_MERGED.fastq.gz
#> 1.0000000 0.5505952
#> AD26-005-H_S10_MERGED.fastq.gz AD26-005-M_S11_MERGED.fastq.gz
#> 0.5505952 0.5505952
#> AD30-ABMX-M_S12_MERGED.fastq.gz AD32-007-M_S13_MERGED.fastq.gz
#> 1.0000000 0.8726415
#> ADABM30X-B_S14_MERGED.fastq.gz ADABM30X-H_S15_MERGED.fastq.gz
#> 0.8726415 0.8726415
#> ADABM30X-M_S16_MERGED.fastq.gz AE30-ABM507_S17_MERGED.fastq.gz
#> 0.7254902 1.0000000
#> B17-014_S18_MERGED.fastq.gz B18-006-B_S19_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> BA16-036bis_S20_MERGED.fastq.gz BA17-050-B_S21_MERGED.fastq.gz
#> 0.7254902 0.7254902
#> BB19-006-H_S22_MERGED.fastq.gz BB6-019-B_S23_MERGED.fastq.gz
#> 0.7254902 1.0000000
#> BB6-019-H_S24_MERGED.fastq.gz BB6-019-M_S25_MERGED.fastq.gz
#> 0.7254902 1.0000000
#> BD14-021_S26_MERGED.fastq.gz BE9-006-B_S27_MERGED.fastq.gz
#> 0.8726415 0.7254902
#> BE9-006-H_S28_MERGED.fastq.gz BE9-006-M_S29_MERGED.fastq.gz
#> 1.0000000 0.8726415
#> BG7-010-B_S30_MERGED.fastq.gz BG7-010-H_S31_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> BG7-010-M_S32_MERGED.fastq.gz BH9-021_S33_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> BJ17-007-M_S34_MERGED.fastq.gz BJ8-ABM-003_S35_MERGED.fastq.gz
#> 1.0000000 0.5505952
#> BL7-006-B_S36_MERGED.fastq.gz BL7-006-H_S37_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> BL7-006-M_S38_MERGED.fastq.gz BN11-041_S39_MERGED.fastq.gz
#> 1.0000000 0.8726415
#> BN9-002_S40_MERGED.fastq.gz BO8-002_S41_MERGED.fastq.gz
#> 0.5505952 0.5505952
#> BO8-005_S42_MERGED.fastq.gz BP11-001-B_S43_MERGED.fastq.gz
#> 0.5505952 0.5505952
#> BP11-001-H_S44_MERGED.fastq.gz BP11-001-M_S45_MERGED.fastq.gz
#> 1.0000000 0.7254902
#> BP12-025-B_S46_MERGED.fastq.gz BP14-006_S47_MERGED.fastq.gz
#> 0.5505952 1.0000000
#> BQ3-019_S48_MERGED.fastq.gz BQ4-018-B_S49_MERGED.fastq.gz
#> 0.7254902 1.0000000
#> BQ4-018-H_S50_MERGED.fastq.gz BQ4-018-M_S51_MERGED.fastq.gz
#> 0.8726415 0.5505952
#> BQ9ABM-002_S52_MERGED.fastq.gz BR8-005_S53_MERGED.fastq.gz
#> 0.8726415 0.5505952
#> BS14-006_S54_MERGED.fastq.gz BT-006-M_S55_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> BT7-006_S56_MERGED.fastq.gz BV11-002-B_S57_MERGED.fastq.gz
#> 1.0000000 0.7254902
#> BV11-002-H_S58_MERGED.fastq.gz BV11-002-M_S59_MERGED.fastq.gz
#> 1.0000000 0.5505952
#> BW8-003_S60_MERGED.fastq.gz C1-001_S61_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> C21-NV1-B_S62_MERGED.fastq.gz C21-NV1-H_S63_MERGED.fastq.gz
#> 0.5505952 0.5505952
#> C21-NV1-M_S64_MERGED.fastq.gz C9-005_S65_MERGED.fastq.gz
#> 0.5505952 0.5505952
#> CA12-024_S66_MERGED.fastq.gz CA9-027_S67_MERGED.fastq.gz
#> 0.7254902 0.5505952
#> CA9-X_S68_MERGED.fastq.gz CB8-019-B_S69_MERGED.fastq.gz
#> 0.8726415 0.5505952
#> CB8-019-H_S70_MERGED.fastq.gz CB8-019-M_S71_MERGED.fastq.gz
#> 0.8726415 0.5505952
#> CB9-013_S72_MERGED.fastq.gz CC3-044_S73_MERGED.fastq.gz
#> 0.7254902 0.7254902
#> CC8-003_S74_MERGED.fastq.gz D17-011_S77_MERGED.fastq.gz
#> 0.5505952 0.8726415
#> D18-003-B_S78_MERGED.fastq.gz D18-003-H_S79_MERGED.fastq.gz
#> 0.5505952 1.0000000
#> D18-003-M_S80_MERGED.fastq.gz D22-NVABM1_S81_MERGED.fastq.gz
#> 0.5505952 0.7254902
#> D61-010-B_S82_MERGED.fastq.gz D9-027-B_S83_MERGED.fastq.gz
#> 0.8726415 1.0000000
#> D9-027-H_S84_MERGED.fastq.gz D9-027-M_S85_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> DBM-ABM-001_S86_MERGED.fastq.gz DJ2-008-B_S87_MERGED.fastq.gz
#> 1.0000000 0.8726415
#> DJ2-008-H_S88_MERGED.fastq.gz DJ2-008-M_S89_MERGED.fastq.gz
#> 0.8726415 1.0000000
#> DP4-ABM001_S90_MERGED.fastq.gz DS1-ABM002-B_S91_MERGED.fastq.gz
#> 0.5505952 0.8726415
#> DS1-ABM002-H_S92_MERGED.fastq.gz DS1-ABM002-M_S93_MERGED.fastq.gz
#> 0.5505952 0.5505952
#> DU3-045-B_S94_MERGED.fastq.gz DW4-007_S95_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> DY5-004-B_S96_MERGED.fastq.gz DY5-004-H_S97_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> DY5-004-M_S98_MERGED.fastq.gz DZ6-ABM-001_S99_MERGED.fastq.gz
#> 1.0000000 0.5505952
#> E9-009-B_S100_MERGED.fastq.gz E9-009-H_S101_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> E9-009-M_S102_MERGED.fastq.gz EA5-ABM-001_S103_MERGED.fastq.gz
#> 1.0000000 0.5505952
#> EC2-013-B_S104_MERGED.fastq.gz F6-ABM-001_S105_MERGED.fastq.gz
#> 0.5505952 0.5505952
#> F7-015-M_S106_MERGED.fastq.gz FOMES19-H_S108_MERGED.fastq.gz
#> 0.5505952 1.0000000
#> FOMES19-M_S109_MERGED.fastq.gz H10-018-M_S110_MERGED.fastq.gz
#> 1.0000000 0.5505952
#> H24-NVABM1-H_S111_MERGED.fastq.gz J18-004-B_S114_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> J18-004-H_S115_MERGED.fastq.gz J18-004-M_S116_MERGED.fastq.gz
#> 0.5505952 1.0000000
#> K18-002-H_S117_MERGED.fastq.gz K26-NVABM1_S118_MERGED.fastq.gz
#> 0.7254902 0.5505952
#> L19X-B_S119_MERGED.fastq.gz L19X-H_S120_MERGED.fastq.gz
#> 0.5505952 0.5505952
#> L19X-M_S121_MERGED.fastq.gz L23-002-B_S122_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> L23-002-H_S123_MERGED.fastq.gz L23-002-M_S124_MERGED.fastq.gz
#> 0.7254902 1.0000000
#> M22-001_S125_MERGED.fastq.gz N19X-B_S126_MERGED.fastq.gz
#> 0.5505952 1.0000000
#> N19X-H_S127_MERGED.fastq.gz N19X-M_S128_MERGED.fastq.gz
#> 1.0000000 0.8726415
#> N22-001-B_S129_MERGED.fastq.gz N23-002-B_S130_MERGED.fastq.gz
#> 0.5505952 0.5505952
#> N23-002-H_S131_MERGED.fastq.gz N23-002-M_S132_MERGED.fastq.gz
#> 0.7254902 0.5505952
#> N25-ABMX_S133_MERGED.fastq.gz NVABM-0058_S134_MERGED.fastq.gz
#> 0.7254902 0.7254902
#> NVABM-0163-H_S135_MERGED.fastq.gz NVABM-0397_S138_MERGED.fastq.gz
#> 0.5505952 0.5505952
#> NVABM0216_S136_MERGED.fastq.gz NVABM0244-M_S137_MERGED.fastq.gz
#> 0.7254902 0.5505952
#> O20-X-B_S139_MERGED.fastq.gz O20-X-H_S140_MERGED.fastq.gz
#> 0.5505952 1.0000000
#> O20-X-M_S141_MERGED.fastq.gz O21-007-B_S142_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> O21-007-H_S143_MERGED.fastq.gz O21-007-M_S144_MERGED.fastq.gz
#> 0.7254902 0.5505952
#> O24-003-B_S145_MERGED.fastq.gz O24-003-H_S146_MERGED.fastq.gz
#> 1.0000000 0.5505952
#> O24-003-M_S147_MERGED.fastq.gz O26-004-B_S148_MERGED.fastq.gz
#> 1.0000000 0.7254902
#> O26-004-H_S149_MERGED.fastq.gz O26-004-M_S150_MERGED.fastq.gz
#> 0.5505952 0.5505952
#> O27-012_S151_MERGED.fastq.gz O9-005-B_S152_MERGED.fastq.gz
#> 0.5505952 1.0000000
#> P19-023-M_S153_MERGED.fastq.gz P27-015-M_S154_MERGED.fastq.gz
#> 0.5505952 0.5505952
#> P27-ABM001_S155_MERGED.fastq.gz Q27-ABM003-B_S156_MERGED.fastq.gz
#> 0.7254902 0.7254902
#> R25-ABMX_S157_MERGED.fastq.gz R28-008-B_S158_MERGED.fastq.gz
#> 0.8726415 1.0000000
#> R28-008-H_S159_MERGED.fastq.gz R28-008-M_S160_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> T28-011_S161_MERGED.fastq.gz T28-ABM602-B_S162_MERGED.fastq.gz
#> 0.5505952 0.5505952
#> U27-ABM002_S163_MERGED.fastq.gz W25-ABMX_S164_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> W26-001-B_S165_MERGED.fastq.gz W26-001-H_S166_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> W26-001-M_S167_MERGED.fastq.gz W30-006_S168_MERGED.fastq.gz
#> 1.0000000 0.8726415
#> W9-025-M_S169_MERGED.fastq.gz X24-009-B_S170_MERGED.fastq.gz
#> 0.5505952 1.0000000
#> X24-009-H_S171_MERGED.fastq.gz X24-009-M_S172_MERGED.fastq.gz
#> 0.5505952 0.5505952
#> X24-010_S173_MERGED.fastq.gz X29-004-B_S174_MERGED.fastq.gz
#> 0.8726415 0.5505952
#> X29-004-H_S175_MERGED.fastq.gz X29-004-M_S176_MERGED.fastq.gz
#> 1.0000000 0.7254902
#> Y21-ABM484-H_S177_MERGED.fastq.gz Y28-002-B_S178_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> Y28-002-H_S179_MERGED.fastq.gz Y28-002-M_S180_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> Y29-007-B_S181_MERGED.fastq.gz Y29-007-H_S182_MERGED.fastq.gz
#> 1.0000000 1.0000000
#> Y29-007-M_S183_MERGED.fastq.gz Y31-ABM484-B_S184_MERGED.fastq.gz
#> 0.7254902 0.7254902
#> Z29-001-H_S185_MERGED.fastq.gz Z30-002_S186_MERGED.fastq.gz
#> 0.8726415 1.0000000
#> Z30-ABM560-M_S187_MERGED.fastq.gz
#> 1.0000000
#>
#> $method
#> [1] "jaccard" "sqrt.D=FALSE"
#>
#> $note
#> [1] "Info -- D is Euclidean because beta.div outputs D[jk] = sqrt(1-S[jk])"
#> [2] "For this D functions, use beta.div with option sqrt.D=FALSE"
#>
#> $D
#> [1] NA
#>
#> attr(,"class")
#> [1] "beta.div"
# }