makeVariantExperimentFromGDS {VariantExperiment} | R Documentation |
Conversion of gds files into SummarizedExperiment object.
makeVariantExperimentFromGDS( file, ftnode, smpnode, assayNames = NULL, rowDataColumns = NULL, colDataColumns = NULL, rowDataOnDisk = TRUE, colDataOnDisk = TRUE, infoColumns = NULL ) makeVariantExperimentFromSEQGDS( file, ftnode = "variant.id", smpnode = "sample.id", assayNames = NULL, rowDataColumns = NULL, colDataColumns = NULL, infoColumns = NULL, rowDataOnDisk = TRUE, colDataOnDisk = TRUE ) makeVariantExperimentFromSNPGDS( file, ftnode = "snp.id", smpnode = "sample.id", assayNames = NULL, rowDataColumns = NULL, colDataColumns = NULL, rowDataOnDisk = TRUE, colDataOnDisk = TRUE )
file |
the GDS file name to be converted. |
ftnode |
the node name for feature id (e.g., "variant.id", "snp.id", etc.). |
smpnode |
the node name for sample id (e.g., "sample.id"). |
assayNames |
the gds node name that will be read into the
|
rowDataColumns |
which columns of |
colDataColumns |
which columns of |
rowDataOnDisk |
whether to save the |
colDataOnDisk |
whether to save the |
infoColumns |
which columns of |
An VariantExperiment
object.
## gds file from DNA-seq data seqfile <- SeqArray::seqExampleFileName(type="gds") ve <- makeVariantExperimentFromGDS(seqfile) ## all assay data names(assays(ve)) showAvailable(seqfile) ## only read specific columns for feature / sample annotation. assayNamess <- showAvailable(seqfile)$assayNames rowdatacols <- showAvailable(seqfile)$rowDataColumns coldatacols <- showAvailable(seqfile)$colDataColumns infocols <- showAvailable(seqfile)$infoColumns ve1 <- makeVariantExperimentFromGDS( seqfile, assayNames = assayNamess[2], rowDataColumns = rowdatacols[1:3], colDataColumns = coldatacols[1], infoColumns = infocols[c(1,3,5,7)], rowDataOnDisk = FALSE, colDataOnDisk = FALSE) assay(ve1) ## the rowData(ve1) and colData(ve1) are now in DataFrame format rowData(ve1) colData(ve1) ## gds file from genotyping data snpfile <- SNPRelate::snpgdsExampleFileName() ve <- makeVariantExperimentFromGDS(snpfile) rowData(ve) colData(ve) metadata(ve) ## Only read specific columns for feature annotation. showAvailable(snpfile) ve1 <- makeVariantExperimentFromGDS(snpfile, rowDataColumns=c("snp.allele")) rowRanges(ve1) ## use specific conversion functions for certain gds types veseq <- makeVariantExperimentFromSEQGDS(seqfile) vesnp <- makeVariantExperimentFromSNPGDS(snpfile)