isa_node_add: Add or remove nodes and properties
In isaeditor: Tools to Manipulate ISA-Tab Files

Description Usage Arguments Details Value See Also Examples

View source: R/isatools.R

Add or remove nodes and properties

isa_node_add(x, node, columns = NULL, after_node = NULL)

isa_node_rm(x, node_id)

isa_property_add(x, property, values = NA, node_id = NULL, after_id = NULL)

isa_property_rm(x, prop_ids = NULL)

`x`	isatab object
`node`	new node identifier (e.g. 'Sample Name')
`columns`	(optional) character vector with columns to add
`after_node`	ID of the node after which the current node should be inserted
`node_id`	ID of the node in which to add the property (default: last node in the isatab).
`property`	Character vector with identifiers (such as 'Comment[Important]') of the properties to be inserted
`values`	vector (if only one property is added) or data frame (if multiple properties are added) of values used to initialize the node / parameter. If multiple properties are added with one call (the length of the `property` vector is greater than one), and values is a data frame, than it has to have sufficient number of columns corresponding to the `property` vector.
`after_id`	ID of the property after which the parameter should be inserted (deault: last property)
`prop_ids`	IDs of the properties to be removed

These functions manipulate the structure of an isatab. isa_node_add and isa_node_rm add or remove whole nodes.

To add or remove properties (individual columns which are not nodes) belonging to a given node, use isa_property_add and isa_property_rm.

Adding and removing nodes is easier using brackets / subscripts. Read the documentation for isatab for details.

Note: IDs are a thing internal to this R package. They are not imported from or exported to actual ISA-tab files. However, given that the node 'identifiers' (e.g. 'Sample Name') can be ambiguous, IDs are necessary to unambiguously identify a node.

These functions return an object of isatab-class.

isatab

file <- system.file('extdata', 's_isatab.txt', package='isaeditor')
isa_s <- read_isa(file)
isa_s <- isa_node_add(isa_s, 'Library Name', columns='Comment[Raw File]')
isa_nodes(isa_s)
isa_s <- isa_property_add(isa_s, 'Characteristics[Age]', values=c(75, 38, 43), node_id='ID1')