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Read Relational Data Values

read_adjacency_list.Rd

Read relational data from a file in adjacency list format and parse it into a LinkMap (or a LinkMap-shaped data.frame). Relies on base::scan and utils::count.fields under the hood.

Usage

read_adjacency_list(
  file,
  sep = "\t",
  quote = "'\"",
  col.names = c("id.x", "id.y"),
  as.df = FALSE,
  ...
)

Arguments

file

the name of a file to read data values from. If the specified file is "", then input is taken from the keyboard (or whatever stdin() reads if input is redirected or R is embedded). (In this case input can be terminated by a blank line or an signal, Ctrl-D on Unix and Ctrl-Z on Windows.)

Otherwise, the file name is interpreted relative to the current working directory (given by getwd()), unless it specifies an absolute path. Tilde-expansion is performed where supported. When running R from a script, file = "stdin" can be used to refer to the process's stdin file stream.

This can be a compressed file (see file).

Alternatively, file can be a connection, which will be opened if necessary, and if so closed at the end of the function call. Whatever mode the connection is opened in, any of , or will be accepted as the marker for a line and so will match sep = "\n".

file can also be a complete URL. (For the supported URL schemes, see the ‘URLs’ section of the help for url.)

To read a data file not in the current encoding (for example a Latin-1 file in a UTF-8 locale or conversely) use a file connection setting its encoding argument (or scan's fileEncoding argument).

sep

the field separator character. Values on each line of the file are separated by this character. (Default: "\t")

quote

the set of quoting characters as a single character string or NULL. In a multibyte locale the quoting characters must be ASCII (single-byte).

col.names

Character vector of length 2, specifying the colnames of the output. (Default: c("id.x", "id.y"))

as.df

Boolean Whether to return an unmodified data.frame or a LinkMap (Default).

...

Additional arguments, passed to scan.

Value

A LinkMap, or if( as.df ), a two-column data.frame formatted like an edge list, appropriate input for LinkMap().

Details

Note that the other common representation of relational data, a two-column table, known as an edge list, can be read in using regular approaches (e.g., ?base::read.table).

See also

utils::count.fields() base::scan()

Examples

# read_adjacency_list(
#     "https://ftp.microbio.me/pub/wol2/function/kegg/ko-to-ec.map"
# )