XenaFilter: Filter a XenaHub Object

Description Usage Arguments Value Author(s) Examples

View source: R/XenaFilter.R

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

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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

Author(s)

Shixiang Wang w_shixiang@163.com

Examples

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# operate TCGA datasets
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
xe
# get all names of clinical data
xe2 = XenaFilter(xe, filterDatasets = "clinical")
datasets(xe2)

ropensci/UCSCXenaTools documentation built on Oct. 6, 2020, 10:05 a.m.