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Save phyloseq object in the form of multiple csv tables.

Source: R/dada_phyloseq.R
write_pq.Rd

[Maturing]

Usage

write_pq(
  physeq,
  path = NULL,
  rdata = FALSE,
  one_file = FALSE,
  write_sam_data = TRUE,
  sam_data_first = FALSE,
  clean_pq = TRUE,
  reorder_asv = FALSE,
  rename_asv = FALSE,
  remove_empty_samples = TRUE,
  remove_empty_taxa = TRUE,
  clean_samples_names = TRUE,
  silent = FALSE,
  verbose = FALSE,
  quote = FALSE,
  sep_csv = "\t",
  ...
)

Arguments

physeq

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

path

a path to the folder to save the phyloseq object

rdata

(logical) does the phyloseq object is also saved in Rdata format?

one_file

(logical) if TRUE, combine all data in one file only

write_sam_data

(logical) does the samples data are add to the file. Only used if one_file is TRUE. Note that these option result in a lot of NA values.

sam_data_first

(logical) if TRUE, put the sample data at the top of the table Only used if one_file and write_sam_data are both TRUE.

clean_pq

(logical) If set to TRUE, empty samples are discarded after subsetting ASV

reorder_asv

(logical) if TRUE the otu_table is ordered by the number of sequences of ASV (descending order). Default to TRUE. Only possible if clean_pq is set to TRUE.

rename_asv

reorder_asv (logical) if TRUE, ASV are renamed by their position in the OTU_table (asv_1, asv_2, ...). Default to FALSE. Only possible if clean_pq is set to TRUE.

remove_empty_samples

(logical) Do you want to remove samples without sequences (this is done after removing empty taxa)

remove_empty_taxa

(logical) Do you want to remove taxa without sequences (this is done before removing empty samples)

clean_samples_names

(logical) Do you want to clean samples names?

silent

(logical) If true, no message are printing.

verbose

(logical) Additional informations in the message the verbose parameter overwrite the silent parameter.

quote

a logical value (default FALSE) or a numeric vector. If TRUE, any character or factor columns will be surrounded by double quotes. If a numeric vector, its elements are taken as the indices of columns to quote. In both cases, row and column names are quoted if they are written. If FALSE nothing is quoted.

sep_csv

(default tabulation) separator for column

...

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

Value

Build a folder (path) containing one to four csv tables (refseq.csv, otu_table.csv, tax_table.csv, sam_data.csv) and if present a phy_tree in Newick format

See also

save_pq()

Author

Adrien Taudière

Examples

write_pq(data_fungi, path = paste0(tempdir(), "/phyloseq"))
#> Cleaning suppress 0 taxa and 0 samples.
write_pq(data_fungi, path = paste0(tempdir(), "/phyloseq"), one_file = TRUE)
#> 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`)`
unlink(paste0(tempdir(), "/phyloseq"), recursive = TRUE)