UCSCXenaTools (version 1.4.8)

XenaFilter: Filter a XenaHub Object

Description

One of main functions in UCSCXenatools. It is used to filter XenaHub object according to cohorts, datasets. All datasets can be found at https://xenabrowser.net/datapages/.

Usage

XenaFilter(
  x,
  filterCohorts = NULL,
  filterDatasets = NULL,
  ignore.case = TRUE,
  ...
)

Arguments

x

a XenaHub object

filterCohorts

default is NULL. A character used to filter cohorts, regular expression is supported.

filterDatasets

default is NULL. A character used to filter datasets, regular expression is supported.

ignore.case

if FALSE, the pattern matching is case sensitive and if TRUE, case is ignored during matching.

...

other arguments except value passed to base::grep().

Value

a XenaHub object

Examples

# NOT RUN {
# operate TCGA datasets
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
xe
# get all names of clinical data
xe2 = XenaFilter(xe, filterDatasets = "clinical")
datasets(xe2)
# }