An R-version-robust drop-in replacement for
phyloseq::rarefy_even_depth(), heavily inspired by that function.
Usage
rarefy_even_depth_pq(
physeq,
sample_size = NULL,
rngseed = FALSE,
replace = TRUE,
trimOTUs = TRUE
)Arguments
- physeq
(required) a
phyloseq-classobject obtained using thephyloseqpackage.- sample_size
(integer) the sequencing depth to rarefy to. If
NULL(default),min(sample_sums(physeq))is used. Samples with fewer reads thansample_sizeare dropped.- rngseed
(logical or integer, default
FALSE) random seed. Set to an integer to seed the RNG before subsampling and restore the caller's global RNG state on exit (matchingphyloseq::rarefy_even_depth()behaviour).FALSEleaves the global RNG untouched.- replace
(logical, default
TRUE) sample with replacement?TRUEmatches thephyloseq::rarefy_even_depth()default.- trimOTUs
(logical, default
TRUE) ifTRUE, taxa that are entirely emptied by subsampling are removed from the returned object.
Value
A new phyloseq-class object with a rarefied
otu_table.
Examples
data_f_rar <- rarefy_even_depth_pq(data_fungi_mini, sample_size = 500)
sample_sums(data_f_rar)
#> A10-005-B_S188_MERGED.fastq.gz A10-005-H_S189_MERGED.fastq.gz
#> 500 500
#> A10-005-M_S190_MERGED.fastq.gz A12-007_S191_MERGED.fastq.gz
#> 500 500
#> A12-007-B_S2_MERGED.fastq.gz A8-005_S4_MERGED.fastq.gz
#> 500 500
#> AB29-ABMX-H_S6_MERGED.fastq.gz AC27-013_S7_MERGED.fastq.gz
#> 500 500
#> AD26-005-H_S10_MERGED.fastq.gz AD26-005-M_S11_MERGED.fastq.gz
#> 500 500
#> AD30-ABMX-M_S12_MERGED.fastq.gz AD32-007-M_S13_MERGED.fastq.gz
#> 500 500
#> ADABM30X-B_S14_MERGED.fastq.gz ADABM30X-H_S15_MERGED.fastq.gz
#> 500 500
#> ADABM30X-M_S16_MERGED.fastq.gz AE30-ABM507_S17_MERGED.fastq.gz
#> 500 500
#> B17-014_S18_MERGED.fastq.gz BA16-036bis_S20_MERGED.fastq.gz
#> 500 500
#> BA17-050-B_S21_MERGED.fastq.gz BB19-006-H_S22_MERGED.fastq.gz
#> 500 500
#> BB6-019-M_S25_MERGED.fastq.gz BD14-021_S26_MERGED.fastq.gz
#> 500 500
#> BJ17-007-M_S34_MERGED.fastq.gz BJ8-ABM-003_S35_MERGED.fastq.gz
#> 500 500
#> BN11-041_S39_MERGED.fastq.gz BO8-002_S41_MERGED.fastq.gz
#> 500 500
#> BP11-001-B_S43_MERGED.fastq.gz BP11-001-H_S44_MERGED.fastq.gz
#> 500 500
#> BP11-001-M_S45_MERGED.fastq.gz BP14-006_S47_MERGED.fastq.gz
#> 500 500
#> BQ4-018-B_S49_MERGED.fastq.gz BQ4-018-H_S50_MERGED.fastq.gz
#> 500 500
#> BQ9ABM-002_S52_MERGED.fastq.gz BS14-006_S54_MERGED.fastq.gz
#> 500 500
#> BV11-002-B_S57_MERGED.fastq.gz BV11-002-H_S58_MERGED.fastq.gz
#> 500 500
#> C1-001_S61_MERGED.fastq.gz C9-005_S65_MERGED.fastq.gz
#> 500 500
#> CA9-X_S68_MERGED.fastq.gz CB9-013_S72_MERGED.fastq.gz
#> 500 500
#> CC3-044_S73_MERGED.fastq.gz D17-011_S77_MERGED.fastq.gz
#> 500 500
#> D18-003-B_S78_MERGED.fastq.gz D22-NVABM1_S81_MERGED.fastq.gz
#> 500 500
#> D61-010-B_S82_MERGED.fastq.gz DBM-ABM-001_S86_MERGED.fastq.gz
#> 500 500
#> DP4-ABM001_S90_MERGED.fastq.gz DS1-ABM002-H_S92_MERGED.fastq.gz
#> 500 500
#> DU3-045-B_S94_MERGED.fastq.gz DW4-007_S95_MERGED.fastq.gz
#> 500 500
#> DZ6-ABM-001_S99_MERGED.fastq.gz EA5-ABM-001_S103_MERGED.fastq.gz
#> 500 500
#> EC2-013-B_S104_MERGED.fastq.gz F6-ABM-001_S105_MERGED.fastq.gz
#> 500 500
#> F7-015-M_S106_MERGED.fastq.gz FOMES19-H_S108_MERGED.fastq.gz
#> 500 500
#> FOMES19-M_S109_MERGED.fastq.gz K26-NVABM1_S118_MERGED.fastq.gz
#> 500 500
#> L19X-H_S120_MERGED.fastq.gz L19X-M_S121_MERGED.fastq.gz
#> 500 500
#> L23-002-H_S123_MERGED.fastq.gz N19X-H_S127_MERGED.fastq.gz
#> 500 500
#> N19X-M_S128_MERGED.fastq.gz N25-ABMX_S133_MERGED.fastq.gz
#> 500 500
#> NVABM-0058_S134_MERGED.fastq.gz O20-X-H_S140_MERGED.fastq.gz
#> 500 500
#> O20-X-M_S141_MERGED.fastq.gz O9-005-B_S152_MERGED.fastq.gz
#> 500 500
#> R25-ABMX_S157_MERGED.fastq.gz T28-011_S161_MERGED.fastq.gz
#> 500 500
#> U27-ABM002_S163_MERGED.fastq.gz W30-006_S168_MERGED.fastq.gz
#> 500 500
#> X24-009-H_S171_MERGED.fastq.gz X24-009-M_S172_MERGED.fastq.gz
#> 500 500
#> X24-010_S173_MERGED.fastq.gz X29-004-M_S176_MERGED.fastq.gz
#> 500 500
#> Y21-ABM484-H_S177_MERGED.fastq.gz Y31-ABM484-B_S184_MERGED.fastq.gz
#> 500 500
#> Z30-ABM560-M_S187_MERGED.fastq.gz
#> 500
# \donttest{
data_f_rar_notrim <- rarefy_even_depth_pq(
data_fungi_mini,
sample_size = 500,
trimOTUs = FALSE
)
# }