showAvailable {VariantExperiment} | R Documentation |
The function to show the available entries for the arguments within
makeVariantExperimentFromGDS
Conversion of gds file into SummarizedExperiment.
showAvailable( file, args = c("name", "rowDataColumns", "colDataColumns", "infoColumns") ) makeVariantExperimentFromGDS( file, name = NULL, rowDataColumns = NULL, colDataColumns = NULL, infoColumns = NULL, rowDataOnDisk = TRUE, colDataOnDisk = TRUE )
file |
the path to the gds.class file. |
args |
the arguments in
|
name |
the components of the gds file that will be represented
as |
rowDataColumns |
which columns of |
colDataColumns |
which columns of |
infoColumns |
which columns of |
rowDataOnDisk |
whether to save the |
colDataOnDisk |
whether to save the |
An VariantExperiment
object.
## snp gds file gds <- SNPRelate::snpgdsExampleFileName() showAvailable(gds) ## sequencing gds file gds <- SeqArray::seqExampleFileName("gds") showAvailable(gds) file <- SNPRelate::snpgdsExampleFileName() ## se <- makeVariantExperimentFromGDS(file) ## rowData(se) ## colData(se) ## metadata(se) ## Only read specific columns for feature annotation. showAvailable(file) ## se1 <- makeVariantExperimentFromGDS(file, rowDataColumns=c("ALLELE")) ## SummarizedExperiment::rowRanges(se1) file <- SeqArray::seqExampleFileName(type="gds") ## se <- makeVariantExperimentFromGDS(file) ## all assay data ## names(assays(se)) ## showAvailable(file) ## only read specific columns for feature / sample annotation. names <- showAvailable(file, "name")$name rowdatacols <- showAvailable(file, "rowDataColumns")$rowDataColumns coldatacols <- showAvailable(file, "colDataColumns")$colDataColumns infocols <- showAvailable(file, "infoColumns")$infoColumns ## se1 <- makeVariantExperimentFromGDS( ## file, ## name = names[2], ## rowDataColumns = rowdatacols[1:3], ## colDataColumns = coldatacols[1], ## infoColumns = infocols[c(1,3,5,7)], ## rowDataOnDisk = FALSE, ## colDataOnDisk = FALSE) ## assay(se1) ## the rowData(se1) and colData(se1) are now in DataFrame format ## rowData(se1) ## colData(se1)