saveVariantExperiment {VariantExperiment} | R Documentation |
saveVariantExperiment Save all the assays in GDS format, including in-memory assays. Delayed assays with delayed operations on them are realized while they are written to disk.
saveVariantExperiment( ve, dir = tempdir(), replace = FALSE, fileFormat = NULL, compress = "LZMA_RA", chunk_size = 10000, rowDataOnDisk = TRUE, colDataOnDisk = TRUE, verbose = FALSE )
ve |
A SummarizedExperiment object, with the array data being ordinary array structure. |
dir |
The directory to save the gds format of the array data, and the newly generated SummarizedExperiment object with array data in GDSArray format. The default is temporary directory within the R session. |
replace |
Whether to replace the directory if it already exists. The default is FALSE. |
fileFormat |
File format for the output gds file. See details. |
compress |
the compression method for writing the gds file. The default is "LZMA_RA". |
chunk_size |
The chunk size (number of rows) when reading
GDSArray-based assays from input |
rowDataOnDisk |
whether to save the |
colDataOnDisk |
whether to save the |
verbose |
whether to print the process messages. The default is FALSE. |
If the input SummarizedExperiment
object has
GDSArray-based assay data, there is no need to specify the
argument fileFomat
. Otherwise, it takes values of
SEQ_ARRAY
for sequencing data or SNP_ARRAY
SNP
array data.
An VariantExperiment
object with the new
gdsfile()
ve.gds
as specified in dir
argument.
gds <- SeqArray::seqExampleFileName("gds") ## ve <- makeVariantExperimentFromGDS(gds) ## gdsfile(ve) ## ve1 <- subsetByOverlaps(ve, GRanges("22:1-48958933")) ## ve1 ## gdsfile(ve1) aa <- tempfile() ## obj <- saveVariantExperiment(ve1, dir=aa, replace=TRUE) ## obj ## gdsfile(obj)