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A wrapper of write_pq to save in all three possible formats

Source: R/dada_phyloseq.R
save_pq.Rd

A wrapper of write_pq to save in all three possible formats

Usage

save_pq(physeq, path = NULL, ...)

Arguments

physeq

(required): a phyloseq-class object obtained using the phyloseq package.

path

a path to the folder to save the phyloseq object

...

Other arguments passed on to write_pq() or utils::write.table() function.

Value

Build a folder (in path) with four csv tables (refseq.csv, otu_table.csv, tax_table.csv, sam_data.csv) + one table with all tables together + a rdata file (physeq.RData) that can be loaded using base::load() function + if present a phylogenetic tree in Newick format (phy_tree.txt)

Details

[Maturing]

Write :

  • 4 separate tables

  • 1 table version

  • 1 RData file

See also

write_pq()

Author

Adrien Taudière

Examples

save_pq(data_fungi, path = paste0(tempdir(), "/phyloseq"))
#> Cleaning suppress 0 taxa and 0 samples.
#> Joining with `by = join_by(`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`, `A12-007-B_S2_MERGED.fastq.gz`,
#> `A15-004_S3_MERGED.fastq.gz`, `A8-005_S4_MERGED.fastq.gz`,
#> `A9-012_S5_MERGED.fastq.gz`, `AB29-ABMX-H_S6_MERGED.fastq.gz`,
#> `AC27-013_S7_MERGED.fastq.gz`, AC29033_S8_MERGED.fastq.gz,
#> `AD26-005-B_S9_MERGED.fastq.gz`, `AD26-005-H_S10_MERGED.fastq.gz`,
#> `AD26-005-M_S11_MERGED.fastq.gz`, `AD30-ABMX-M_S12_MERGED.fastq.gz`,
#> `AD32-007-M_S13_MERGED.fastq.gz`, `ADABM30X-B_S14_MERGED.fastq.gz`,
#> `ADABM30X-H_S15_MERGED.fastq.gz`, `ADABM30X-M_S16_MERGED.fastq.gz`,
#> `AE30-ABM507_S17_MERGED.fastq.gz`, `B17-014_S18_MERGED.fastq.gz`,
#> `B18-006-B_S19_MERGED.fastq.gz`, `BA16-036bis_S20_MERGED.fastq.gz`,
#> `BA17-050-B_S21_MERGED.fastq.gz`, `BB19-006-H_S22_MERGED.fastq.gz`,
#> `BB6-019-B_S23_MERGED.fastq.gz`, `BB6-019-H_S24_MERGED.fastq.gz`,
#> `BB6-019-M_S25_MERGED.fastq.gz`, `BD14-021_S26_MERGED.fastq.gz`,
#> `BE9-006-B_S27_MERGED.fastq.gz`, `BE9-006-H_S28_MERGED.fastq.gz`,
#> `BE9-006-M_S29_MERGED.fastq.gz`, `BG7-010-B_S30_MERGED.fastq.gz`,
#> `BG7-010-H_S31_MERGED.fastq.gz`, `BG7-010-M_S32_MERGED.fastq.gz`,
#> `BH9-021_S33_MERGED.fastq.gz`, `BJ17-007-M_S34_MERGED.fastq.gz`,
#> `BJ8-ABM-003_S35_MERGED.fastq.gz`, `BL7-006-B_S36_MERGED.fastq.gz`,
#> `BL7-006-H_S37_MERGED.fastq.gz`, `BL7-006-M_S38_MERGED.fastq.gz`,
#> `BN11-041_S39_MERGED.fastq.gz`, `BN9-002_S40_MERGED.fastq.gz`,
#> `BO8-002_S41_MERGED.fastq.gz`, `BO8-005_S42_MERGED.fastq.gz`,
#> `BP11-001-B_S43_MERGED.fastq.gz`, `BP11-001-H_S44_MERGED.fastq.gz`,
#> `BP11-001-M_S45_MERGED.fastq.gz`, `BP12-025-B_S46_MERGED.fastq.gz`,
#> `BP14-006_S47_MERGED.fastq.gz`, `BQ3-019_S48_MERGED.fastq.gz`,
#> `BQ4-018-B_S49_MERGED.fastq.gz`, `BQ4-018-H_S50_MERGED.fastq.gz`,
#> `BQ4-018-M_S51_MERGED.fastq.gz`, `BQ9ABM-002_S52_MERGED.fastq.gz`,
#> `BR8-005_S53_MERGED.fastq.gz`, `BS14-006_S54_MERGED.fastq.gz`,
#> `BT-006-M_S55_MERGED.fastq.gz`, `BT7-006_S56_MERGED.fastq.gz`,
#> `BV11-002-B_S57_MERGED.fastq.gz`, `BV11-002-H_S58_MERGED.fastq.gz`,
#> `BV11-002-M_S59_MERGED.fastq.gz`, `BW8-003_S60_MERGED.fastq.gz`,
#> `C1-001_S61_MERGED.fastq.gz`, `C21-NV1-B_S62_MERGED.fastq.gz`,
#> `C21-NV1-H_S63_MERGED.fastq.gz`, `C21-NV1-M_S64_MERGED.fastq.gz`,
#> `C9-005_S65_MERGED.fastq.gz`, `CA12-024_S66_MERGED.fastq.gz`,
#> `CA9-027_S67_MERGED.fastq.gz`, `CA9-X_S68_MERGED.fastq.gz`,
#> `CB8-019-B_S69_MERGED.fastq.gz`, `CB8-019-H_S70_MERGED.fastq.gz`,
#> `CB8-019-M_S71_MERGED.fastq.gz`, `CB9-013_S72_MERGED.fastq.gz`,
#> `CC3-044_S73_MERGED.fastq.gz`, `CC8-003_S74_MERGED.fastq.gz`,
#> `D17-011_S77_MERGED.fastq.gz`, `D18-003-B_S78_MERGED.fastq.gz`,
#> `D18-003-H_S79_MERGED.fastq.gz`, `D18-003-M_S80_MERGED.fastq.gz`,
#> `D22-NVABM1_S81_MERGED.fastq.gz`, `D61-010-B_S82_MERGED.fastq.gz`,
#> `D9-027-B_S83_MERGED.fastq.gz`, `D9-027-H_S84_MERGED.fastq.gz`,
#> `D9-027-M_S85_MERGED.fastq.gz`, `DBM-ABM-001_S86_MERGED.fastq.gz`,
#> `DJ2-008-B_S87_MERGED.fastq.gz`, `DJ2-008-H_S88_MERGED.fastq.gz`,
#> `DJ2-008-M_S89_MERGED.fastq.gz`, `DP4-ABM001_S90_MERGED.fastq.gz`,
#> `DS1-ABM002-B_S91_MERGED.fastq.gz`, `DS1-ABM002-H_S92_MERGED.fastq.gz`,
#> `DS1-ABM002-M_S93_MERGED.fastq.gz`, `DU3-045-B_S94_MERGED.fastq.gz`,
#> `DW4-007_S95_MERGED.fastq.gz`, `DY5-004-B_S96_MERGED.fastq.gz`,
#> `DY5-004-H_S97_MERGED.fastq.gz`, `DY5-004-M_S98_MERGED.fastq.gz`,
#> `DZ6-ABM-001_S99_MERGED.fastq.gz`, `E9-009-B_S100_MERGED.fastq.gz`,
#> `E9-009-H_S101_MERGED.fastq.gz`, `E9-009-M_S102_MERGED.fastq.gz`,
#> `EA5-ABM-001_S103_MERGED.fastq.gz`, `EC2-013-B_S104_MERGED.fastq.gz`,
#> `F6-ABM-001_S105_MERGED.fastq.gz`, `F7-015-M_S106_MERGED.fastq.gz`,
#> `FOMES19-H_S108_MERGED.fastq.gz`, `FOMES19-M_S109_MERGED.fastq.gz`,
#> `H10-018-M_S110_MERGED.fastq.gz`, `H24-NVABM1-H_S111_MERGED.fastq.gz`,
#> `J18-004-B_S114_MERGED.fastq.gz`, `J18-004-H_S115_MERGED.fastq.gz`,
#> `J18-004-M_S116_MERGED.fastq.gz`, `K18-002-H_S117_MERGED.fastq.gz`,
#> `K26-NVABM1_S118_MERGED.fastq.gz`, `L19X-B_S119_MERGED.fastq.gz`,
#> `L19X-H_S120_MERGED.fastq.gz`, `L19X-M_S121_MERGED.fastq.gz`,
#> `L23-002-B_S122_MERGED.fastq.gz`, `L23-002-H_S123_MERGED.fastq.gz`,
#> `L23-002-M_S124_MERGED.fastq.gz`, `M22-001_S125_MERGED.fastq.gz`,
#> `N19X-B_S126_MERGED.fastq.gz`, `N19X-H_S127_MERGED.fastq.gz`,
#> `N19X-M_S128_MERGED.fastq.gz`, `N22-001-B_S129_MERGED.fastq.gz`,
#> `N23-002-B_S130_MERGED.fastq.gz`, `N23-002-H_S131_MERGED.fastq.gz`,
#> `N23-002-M_S132_MERGED.fastq.gz`, `N25-ABMX_S133_MERGED.fastq.gz`,
#> `NVABM-0058_S134_MERGED.fastq.gz`, `NVABM-0163-H_S135_MERGED.fastq.gz`,
#> `NVABM-0397_S138_MERGED.fastq.gz`, NVABM0216_S136_MERGED.fastq.gz,
#> `NVABM0244-M_S137_MERGED.fastq.gz`, `O20-X-B_S139_MERGED.fastq.gz`,
#> `O20-X-H_S140_MERGED.fastq.gz`, `O20-X-M_S141_MERGED.fastq.gz`,
#> `O21-007-B_S142_MERGED.fastq.gz`, `O21-007-H_S143_MERGED.fastq.gz`,
#> `O21-007-M_S144_MERGED.fastq.gz`, `O24-003-B_S145_MERGED.fastq.gz`,
#> `O24-003-H_S146_MERGED.fastq.gz`, `O24-003-M_S147_MERGED.fastq.gz`,
#> `O26-004-B_S148_MERGED.fastq.gz`, `O26-004-H_S149_MERGED.fastq.gz`,
#> `O26-004-M_S150_MERGED.fastq.gz`, `O27-012_S151_MERGED.fastq.gz`,
#> `O9-005-B_S152_MERGED.fastq.gz`, `P19-023-M_S153_MERGED.fastq.gz`,
#> `P27-015-M_S154_MERGED.fastq.gz`, `P27-ABM001_S155_MERGED.fastq.gz`,
#> `Q27-ABM003-B_S156_MERGED.fastq.gz`, `R25-ABMX_S157_MERGED.fastq.gz`,
#> `R28-008-B_S158_MERGED.fastq.gz`, `R28-008-H_S159_MERGED.fastq.gz`,
#> `R28-008-M_S160_MERGED.fastq.gz`, `T28-011_S161_MERGED.fastq.gz`,
#> `T28-ABM602-B_S162_MERGED.fastq.gz`, `U27-ABM002_S163_MERGED.fastq.gz`,
#> `W25-ABMX_S164_MERGED.fastq.gz`, `W26-001-B_S165_MERGED.fastq.gz`,
#> `W26-001-H_S166_MERGED.fastq.gz`, `W26-001-M_S167_MERGED.fastq.gz`,
#> `W30-006_S168_MERGED.fastq.gz`, `W9-025-M_S169_MERGED.fastq.gz`,
#> `X24-009-B_S170_MERGED.fastq.gz`, `X24-009-H_S171_MERGED.fastq.gz`,
#> `X24-009-M_S172_MERGED.fastq.gz`, `X24-010_S173_MERGED.fastq.gz`,
#> `X29-004-B_S174_MERGED.fastq.gz`, `X29-004-H_S175_MERGED.fastq.gz`,
#> `X29-004-M_S176_MERGED.fastq.gz`, `Y21-ABM484-H_S177_MERGED.fastq.gz`,
#> `Y28-002-B_S178_MERGED.fastq.gz`, `Y28-002-H_S179_MERGED.fastq.gz`,
#> `Y28-002-M_S180_MERGED.fastq.gz`, `Y29-007-B_S181_MERGED.fastq.gz`,
#> `Y29-007-H_S182_MERGED.fastq.gz`, `Y29-007-M_S183_MERGED.fastq.gz`,
#> `Y31-ABM484-B_S184_MERGED.fastq.gz`, `Z29-001-H_S185_MERGED.fastq.gz`,
#> `Z30-002_S186_MERGED.fastq.gz`, `Z30-ABM560-M_S187_MERGED.fastq.gz`)`
#> Cleaning suppress 0 taxa and 0 samples.
unlink(paste0(tempdir(), "/phyloseq"), recursive = TRUE)