Export data from R

Usage

export(object, con, ...)

# S4 method for DESeqAnalysis,character
export(object, con, compress = FALSE, overwrite = TRUE, quiet = FALSE)

# S4 method for DESeqDataSet,character
export(object, con, compress = FALSE, overwrite = TRUE, quiet = FALSE)

Arguments

object: Object.
con: character(1). Directory path.
compress: logical(1). Apply gzip compression to all files.
overwrite: logical(1). Overwrite existing file on disk.
quiet: logical(1). Perform command quietly, suppressing messages.
...: Additional arguments.

Value

Invisible character or list of file paths.

Details

Size-factor normalized coutns and FPKM values are calculated on the fly and exported automatically.

Note

Updated 2022-09-13.

Examples

data(deseq)

## DESeqAnalysis ====
con <- AcidBase::tempdir2()
x <- export(deseq, con = con)
#> → Exporting <DESeqDataSet> to data.
#> → Exporting <SummarizedExperiment> to /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/data.
#> → Exporting assays "counts", "normalized", "fpkm" to /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/data/assays.
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/data/assays/counts.csv using base::`write.table()`.
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/data/assays/normalized.csv using base::`write.table()`.
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/data/assays/fpkm.csv using base::`write.table()`.
#> ℹ Dropping 2 non-atomic columns: "geneSynonyms", "ncbiGeneId".
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/data/rowData.csv using base::`write.table()`.
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/data/colData.csv using base::`write.table()`.
#> → Exporting <DESeqTransform> to transform.
#> → Exporting <SummarizedExperiment> to /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/transform.
#> → Exporting assays "assay" to /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/transform/assays.
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/transform/assays/assay.csv using base::`write.table()`.
#> ℹ Dropping 2 non-atomic columns: "geneSynonyms", "ncbiGeneId".
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/transform/rowData.csv using base::`write.table()`.
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/transform/colData.csv using base::`write.table()`.
#> → Exporting `DESeqResults` tables to resultsTables.
#> ℹ 30 differentially expressed genes (alpha < 0.01).
#> ℹ 17 upregulated genes (alpha < 0.01).
#> ℹ 13 downregulated genes (alpha < 0.01).
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsTables/condition_B_vs_A/all.csv using base::`write.table()`.
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsTables/condition_B_vs_A/up.csv using base::`write.table()`.
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsTables/condition_B_vs_A/down.csv using base::`write.table()`.
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsTables/condition_B_vs_A/both.csv using base::`write.table()`.
#> ℹ 0 differentially expressed genes (alpha < 0.01).
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsTables/treatment_D_vs_C/all.csv using base::`write.table()`.
#> → Exporting <DESeqResults> matrices to resultsMatrices.
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsMatrices/log2FoldChange.csv using base::`write.table()`.
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsMatrices/stat.csv using base::`write.table()`.
#> → Exporting /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsMatrices/padj.csv using base::`write.table()`.
print(x)
#> $data
#> $data$assays
#> $data$assays$counts
#> [1] "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/data/assays/counts.csv"
#> 
#> $data$assays$normalized
#> [1] "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/data/assays/normalized.csv"
#> 
#> $data$assays$fpkm
#> [1] "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/data/assays/fpkm.csv"
#> 
#> 
#> $data$rowData
#> [1] "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/data/rowData.csv"
#> 
#> $data$colData
#> [1] "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/data/colData.csv"
#> 
#> 
#> $transform
#> $transform$assays
#> $transform$assays$assay
#> [1] "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/transform/assays/assay.csv"
#> 
#> 
#> $transform$rowData
#> [1] "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/transform/rowData.csv"
#> 
#> $transform$colData
#> [1] "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/transform/colData.csv"
#> 
#> 
#> $resultsTables
#> $resultsTables$condition_B_vs_A
#>                                                                                                                                      all 
#>  "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsTables/condition_B_vs_A/all.csv" 
#>                                                                                                                                       up 
#>   "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsTables/condition_B_vs_A/up.csv" 
#>                                                                                                                                     down 
#> "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsTables/condition_B_vs_A/down.csv" 
#>                                                                                                                                     both 
#> "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsTables/condition_B_vs_A/both.csv" 
#> 
#> $resultsTables$treatment_D_vs_C
#>                                                                                                                                     all 
#> "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsTables/treatment_D_vs_C/all.csv" 
#> 
#> 
#> $resultsMatrices
#>                                                                                                                      log2FoldChange 
#> "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsMatrices/log2FoldChange.csv" 
#>                                                                                                                                stat 
#>           "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsMatrices/stat.csv" 
#>                                                                                                                                padj 
#>           "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpaRGehr/xedyAXQjDR-171157275904613/resultsMatrices/padj.csv" 
#> 
AcidBase::unlink2(con)