R Interface to CoreArray Genomic Data Structure (GDS) Files


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Documentation for package ‘gdsfmt’ version 1.6.2

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gdsfmt-package R Interface to CoreArray Genomic Data Structure (GDS) files
add.gdsn Add a new GDS node
addfile.gdsn Add a GDS node with a file
addfolder.gdsn Add a folder to the GDS node
append.gdsn Append data to a specified variable
apply.gdsn Apply functions over margins
assign.gdsn Assign/append data to a GDS node
cache.gdsn Caching variable data
cleanup.gds Clean up fragments
closefn.gds Close a GDS file
clusterApply.gdsn Apply functions over matrix margins in parallel
cnt.gdsn Return the number of child nodes
compression.gdsn Modify compression mode
copyto.gdsn Copy GDS nodes
createfn.gds Create a GDS file
delete.attr.gdsn Delete attribute(s)
delete.gdsn Delete a GDS node
diagnosis.gds Diagnose the GDS file
gds.class the class of GDS file
gdsfmt R Interface to CoreArray Genomic Data Structure (GDS) files
gdsn.class the class of variable node in the GDS file
get.attr.gdsn Get attributes
getfile.gdsn Output a file from a stream container
getfolder.gdsn Get the folder
index.gdsn Return the specified node
is.element.gdsn whether the elements are in a set
lasterr.gds Return the last error message
ls.gdsn Return the names of child nodes
moveto.gdsn Relocate a GDS node
name.gdsn Return the variable name of a node
objdesp.gdsn Variable description
openfn.gds Open a GDS file
permdim.gdsn Array Transposition
print.gds.class Show the information of class "gds.class" and "gdsn.class"
print.gdsn.class Show the information of class "gds.class" and "gdsn.class"
put.attr.gdsn Add an attribute into a GDS node
read.gdsn Read data field of a GDS node
readex.gdsn Read data field of a GDS node with a selection
readmode.gdsn Switch to read mode in the compression settings
rename.gdsn Rename a GDS node
setdim.gdsn Set the dimension of data field
showfile.gds Enumerate opened GDS files
sync.gds Synchronize a GDS file
system.gds Get the parameters in the GDS system
write.gdsn Write data to a GDS node