Returns a list of track names

Returns a list of track names in Genomic Database.

gtrack.ls(
  ...,
  pattern = NULL,
  db = NULL,
  ignore.case = FALSE,
  perl = FALSE,
  fixed = FALSE,
  useBytes = FALSE
)

Arguments

...

additional arguments of either form 'pattern' (matched against track names) or 'attribute = pattern' (matched against a track attribute value)

pattern

optional pattern to match against track names, equivalent to passing it positionally (e.g. gtrack.ls("den*") and gtrack.ls(pattern = "den*") are the same). Note that this means a track attribute literally named "pattern" can no longer be filtered by name via ...; use gtrack.ls() followed by gtrack.attr.get instead.

db

optional database path to filter tracks. If specified, only tracks from that database are returned.

ignore.case, perl, fixed, useBytes

see 'grep'

Value

An array that contains the names of tracks that match the supplied patterns.

Details

This function returns a list of tracks whose name or track attribute value match a pattern (see 'grep'). If called without any arguments all tracks are returned.

If pattern is specified without a track attribute (i.e. in the form of 'pattern', either positionally or via the 'pattern' argument) then filtering is applied to the track names. If pattern is supplied with a track attribute (i.e. in the form of 'name = pattern') then track attribute is matched against the pattern.

Multiple patterns are applied one after another. The resulted list of tracks should match all the patterns.

When multiple databases are connected, the 'db' parameter can be used to filter tracks to only those from a specific database.

See also

grep, gtrack.exists, gtrack.create, gtrack.rm, gtrack.dataset

Examples

gdb.init_examples()

# get all track names
gtrack.ls()
#> [1] "array_track"         "dense_track"         "rects_track"        
#> [4] "sparse_track"        "subdir.dense_track2"

# get track names that match the pattern "den*"
gtrack.ls("den*")
#> [1] "dense_track"         "subdir.dense_track2"

# equivalent, using the 'pattern' argument
gtrack.ls(pattern = "den*")
#> [1] "dense_track"         "subdir.dense_track2"

# get track names whose "created.by" attribute match the pattern
# "create_sparse"
gtrack.ls(created.by = "create_sparse")
#> [1] "sparse_track"

# get track names whose names match the pattern "den*" and whose
# "created.by" attribute match the pattern "track"
gtrack.ls("den*", created.by = "track")
#> [1] "subdir.dense_track2"