Package 'UCSCXenaTools' reference manual

Title:	Download and Explore Datasets from UCSC Xena Data Hubs
Description:	Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
Authors:	Shixiang Wang [aut, cre] , Xue-Song Liu [aut] , Martin Morgan [ctb], Christine Stawitz [rev] (Christine reviewed the package for ropensci, see <https://github.com/ropensci/software-review/issues/315>), Carl Ganz [rev] (Carl reviewed the package for ropensci, see <https://github.com/ropensci/software-review/issues/315>)
Maintainer:	Shixiang Wang <[email protected]>
License:	GPL-3
Version:	1.5.0
Built:	2024-08-29 08:24:38 UTC
Source:	https://github.com/ropensci/UCSCXenaTools

Get or Check TCGA Available ProjectID, DataType and FileType

Description

Get or Check TCGA Available ProjectID, DataType and FileType

Usage

availTCGA(which = c("all", "ProjectID", "DataType", "FileType"))
availTCGA(which = c("all", "ProjectID", "DataType", "FileType"))

Arguments

which

a character of c("All", "ProjectID", "DataType", "FileType")

Author(s)

Shixiang Wang [email protected]

Examples


availTCGA("all")

availTCGA("all")

Get cohorts of XenaHub object

Description

Get cohorts of XenaHub object

Usage

cohorts(x)
cohorts(x)

Arguments

`x`	a XenaHub object

Value

a character vector contains cohorts

Examples

xe = XenaGenerate(subset = XenaHostNames == "tcgaHub"); cohorts(xe)
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub"); cohorts(xe)

Get datasets of XenaHub object

Description

Get datasets of XenaHub object

Usage

datasets(x)
datasets(x)

Arguments

`x`	a XenaHub object

Value

a character vector contains datasets

Examples

xe = XenaGenerate(subset = XenaHostNames == "tcgaHub"); datasets(xe)
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub"); datasets(xe)

Easily Download TCGA Data by Several Options

Description

TCGA is a very useful database and here we provide this function to download TCGA (include TCGA Pancan) datasets in human-friendly way. Users who are not familiar with R operation will benefit from this.

Usage

downloadTCGA(
  project = NULL,
  data_type = NULL,
  file_type = NULL,
  destdir = tempdir(),
  force = FALSE,
  ...
)
downloadTCGA(
  project = NULL,
  data_type = NULL,
  file_type = NULL,
  destdir = tempdir(),
  force = FALSE,
  ...
)

Arguments

`project`	default is `NULL`. Should be one or more of TCGA project id (character vector) provided by Xena. See all available project id, please use `availTCGA("ProjectID")`.
`data_type`	default is `NULL`. Should be a character vector specify data type. See all available data types by `availTCGA("DataType")`.
`file_type`	default is `NULL`. Should be a character vector specify file type. See all available file types by `availTCGA("FileType")`.
`destdir`	specify a location to store download data. Default is system temp directory.
`force`	logical. if `TRUE`, force to download data no matter whether files exist. Default is `FALSE`.
`...`	other argument to `download.file` function

Details

All availble information about datasets of TCGA can access vis availTCGA() and check with showTCGA().

Value

same as XenaDownload() function result.

Author(s)

Shixiang Wang [email protected]

Examples

## Not run: 
# download RNASeq data (use UVM as example)
downloadTCGA(project = "UVM",
                 data_type = "Gene Expression RNASeq",
                 file_type = "IlluminaHiSeq RNASeqV2")

## End(Not run)
## Not run: 
# download RNASeq data (use UVM as example)
downloadTCGA(project = "UVM",
                 data_type = "Gene Expression RNASeq",
                 file_type = "IlluminaHiSeq RNASeqV2")

## End(Not run)

Fetch Data from UCSC Xena Hosts

Description

When you want to query just data for several genes/samples from UCSC Xena datasets, a better way is to use these fetch_ functions instead of downloading a whole dataset. Details about functions please see the following sections.

Usage

fetch(host, dataset)

fetch_dense_values(
  host,
  dataset,
  identifiers = NULL,
  samples = NULL,
  check = TRUE,
  use_probeMap = FALSE,
  time_limit = 30
)

fetch_sparse_values(host, dataset, genes, samples = NULL, time_limit = 30)

fetch_dataset_samples(host, dataset, limit = NULL)

fetch_dataset_identifiers(host, dataset)

has_probeMap(host, dataset, return_url = FALSE)
fetch(host, dataset)

fetch_dense_values(
  host,
  dataset,
  identifiers = NULL,
  samples = NULL,
  check = TRUE,
  use_probeMap = FALSE,
  time_limit = 30
)

fetch_sparse_values(host, dataset, genes, samples = NULL, time_limit = 30)

fetch_dataset_samples(host, dataset, limit = NULL)

fetch_dataset_identifiers(host, dataset)

has_probeMap(host, dataset, return_url = FALSE)

Arguments

`host`	a UCSC Xena host, like "https://toil.xenahubs.net". All available hosts can be printed by `xena_default_hosts()`.
`dataset`	a UCSC Xena dataset, like "tcga_RSEM_gene_tpm". All available datasets can be printed by running `XenaData$XenaDatasets` or obtained from UCSC Xena datapages.
`identifiers`	Identifiers could be probe (like "ENSG00000000419.12"), gene (like "TP53") etc.. If it is `NULL`, all identifiers in the dataset will be used.
`samples`	ID of samples, like "TCGA-02-0047-01". If it is `NULL`, all samples in the dataset will be used. However, it is better to download the whole datasets if you query many samples and genes.
`check`	if `TRUE`, check whether specified `identifiers` and `samples` exist the dataset (all failed items will be filtered out). However, if `FALSE`, the code is much faster.
`use_probeMap`	if `TRUE`, will check if the dataset has ProbeMap firstly. When the dataset you want to query has a identifier-to-gene mapping, identifiers can be gene symbols even the identifiers of dataset are probes or others.
`time_limit`	time limit for getting response in seconds.
`genes`	gene names.
`limit`	number of samples, if `NULL`, return all samples.
`return_url`	if `TRUE`, returns the info of probeMap instead of a logical value when the result exists.

Details

There are three primary data types: dense matrix (samples by probes (or say identifiers)), sparse (sample, position, variant), and segmented (sample, position, value).

Dense matrices can be genotypic or phenotypic, it is a sample-by-identifiers matrix. Phenotypic matrices have associated field metadata (descriptive names, codes, etc.). Genotypic matricies may have an associated probeMap, which maps probes to genomic locations. If a matrix has hugo probeMap, the probes themselves are gene names. Otherwise, a probeMap is used to map a gene location to a set of probes.

Value

a matirx or character vector or a list.

Functions

fetch_dense_values(): fetches values from a dense matrix.
fetch_sparse_values(): fetches values from a sparse data.frame.
fetch_dataset_samples(): fetches samples from a dataset
fetch_dataset_identifiers(): fetches identifies from a dataset.
has_probeMap(): checks if a dataset has ProbeMap.

Examples

library(UCSCXenaTools)

host <- "https://toil.xenahubs.net"
dataset <- "tcga_RSEM_gene_tpm"
samples <- c("TCGA-02-0047-01", "TCGA-02-0055-01", "TCGA-02-2483-01", "TCGA-02-2485-01")
probes <- c("ENSG00000282740.1", "ENSG00000000005.5", "ENSG00000000419.12")
genes <- c("TP53", "RB1", "PIK3CA")


# Fetch samples
fetch_dataset_samples(host, dataset, 2)
# Fetch identifiers
fetch_dataset_identifiers(host, dataset)
# Fetch expression value by probes
fetch_dense_values(host, dataset, probes, samples, check = FALSE)
# Fetch expression value by gene symbol (if the dataset has probeMap)
has_probeMap(host, dataset)
fetch_dense_values(host, dataset, genes, samples, check = FALSE, use_probeMap = TRUE)

library(UCSCXenaTools)

host <- "https://toil.xenahubs.net"
dataset <- "tcga_RSEM_gene_tpm"
samples <- c("TCGA-02-0047-01", "TCGA-02-0055-01", "TCGA-02-2483-01", "TCGA-02-2485-01")
probes <- c("ENSG00000282740.1", "ENSG00000000005.5", "ENSG00000000419.12")
genes <- c("TP53", "RB1", "PIK3CA")


# Fetch samples
fetch_dataset_samples(host, dataset, 2)
# Fetch identifiers
fetch_dataset_identifiers(host, dataset)
# Fetch expression value by probes
fetch_dense_values(host, dataset, probes, samples, check = FALSE)
# Fetch expression value by gene symbol (if the dataset has probeMap)
has_probeMap(host, dataset)
fetch_dense_values(host, dataset, genes, samples, check = FALSE, use_probeMap = TRUE)

Get TCGA Common Data Sets by Project ID and Property

Description

This is the most useful function for user to download common TCGA datasets, it is similar to getFirehoseData function in RTCGAToolbox package.

Usage

getTCGAdata(
  project = NULL,
  clinical = TRUE,
  download = FALSE,
  forceDownload = FALSE,
  destdir = tempdir(),
  mRNASeq = FALSE,
  mRNAArray = FALSE,
  mRNASeqType = "normalized",
  miRNASeq = FALSE,
  exonRNASeq = FALSE,
  RPPAArray = FALSE,
  ReplicateBaseNormalization = FALSE,
  Methylation = FALSE,
  MethylationType = c("27K", "450K"),
  GeneMutation = FALSE,
  SomaticMutation = FALSE,
  GisticCopyNumber = FALSE,
  Gistic2Threshold = TRUE,
  CopyNumberSegment = FALSE,
  RemoveGermlineCNV = TRUE,
  ...
)
getTCGAdata(
  project = NULL,
  clinical = TRUE,
  download = FALSE,
  forceDownload = FALSE,
  destdir = tempdir(),
  mRNASeq = FALSE,
  mRNAArray = FALSE,
  mRNASeqType = "normalized",
  miRNASeq = FALSE,
  exonRNASeq = FALSE,
  RPPAArray = FALSE,
  ReplicateBaseNormalization = FALSE,
  Methylation = FALSE,
  MethylationType = c("27K", "450K"),
  GeneMutation = FALSE,
  SomaticMutation = FALSE,
  GisticCopyNumber = FALSE,
  Gistic2Threshold = TRUE,
  CopyNumberSegment = FALSE,
  RemoveGermlineCNV = TRUE,
  ...
)

Arguments

`project`	default is `NULL`. Should be one or more of TCGA project id (character vector) provided by Xena. See all available project id, please use `availTCGA("ProjectID")`.
`clinical`	logical. if `TRUE`, download clinical information. Default is `TRUE`.
`download`	logical. if `TRUE`, download data, otherwise return a result list include data information. Default is `FALSE`. You can set this to `FALSE` if you want to check what you will download or use other function provided by `UCSCXenaTools` to filter result datasets you want to download.
`forceDownload`	logical. if `TRUE`, force to download files no matter if exist. Default is `FALSE`.
`destdir`	specify a location to store download data. Default is system temp directory.
`mRNASeq`	logical. if `TRUE`, download mRNASeq data. Default is `FALSE`.
`mRNAArray`	logical. if `TRUE`, download mRNA microarray data. Default is `FALSE`.
`mRNASeqType`	character vector. Can be one, two or three in `c("normalized", "pancan normalized", "percentile")`.
`miRNASeq`	logical. if `TRUE`, download miRNASeq data. Default is `FALSE`.
`exonRNASeq`	logical. if `TRUE`, download exon RNASeq data. Default is `FALSE`.
`RPPAArray`	logical. if `TRUE`, download RPPA data. Default is `FALSE`.
`ReplicateBaseNormalization`	logical. if `TRUE`, download RPPA data by Replicate Base Normalization (RBN). Default is `FALSE`.
`Methylation`	logical. if `TRUE`, download DNA Methylation data. Default is `FALSE`.
`MethylationType`	character vector. Can be one or two in `c("27K", "450K")`.
`GeneMutation`	logical. if `TRUE`, download gene mutation data. Default is `FALSE`.
`SomaticMutation`	logical. if `TRUE`, download somatic mutation data. Default is `FALSE`.
`GisticCopyNumber`	logical. if `TRUE`, download Gistic2 Copy Number data. Default is `FALSE`.
`Gistic2Threshold`	logical. if `TRUE`, download Threshold Gistic2 data. Default is `TRUE`.
`CopyNumberSegment`	logical. if `TRUE`, download Copy Number Segment data. Default is `FALSE`.
`RemoveGermlineCNV`	logical. if `TRUE`, download Copy Number Segment data which has removed germline copy number variation. Default is `TRUE`.
`...`	other argument to `download.file` function

Details

TCGA Common Data Sets are frequently used for biological analysis. To make easier to achieve these data, this function provide really easy options to choose datasets and behavior. All availble information about datasets of TCGA can access vis availTCGA() and check with showTCGA().

Value

if download=TRUE, return data.frame from XenaDownload, otherwise return a list including XenaHub object and datasets information

Author(s)

Shixiang Wang [email protected]

Examples

###### get data, but not download

# 1 choose project and data types you wanna download
getTCGAdata(project = "LUAD", mRNASeq = TRUE, mRNAArray = TRUE,
mRNASeqType = "normalized", miRNASeq = TRUE, exonRNASeq = TRUE,
RPPAArray = TRUE, Methylation = TRUE, MethylationType = "450K",
GeneMutation = TRUE, SomaticMutation = TRUE)

# 2 only choose 'LUAD' and its clinical data
getTCGAdata(project = "LUAD")
## Not run: 
###### download datasets

# 3 download clinical datasets of LUAD and LUSC
getTCGAdata(project = c("LUAD", "LUSC"), clinical = TRUE, download = TRUE)

# 4 download clinical, RPPA and gene mutation datasets of LUAD and LUSC
# getTCGAdata(project = c("LUAD", "LUSC"), clinical = TRUE, RPPAArray = TRUE, GeneMutation = TRUE)

## End(Not run)
###### get data, but not download

# 1 choose project and data types you wanna download
getTCGAdata(project = "LUAD", mRNASeq = TRUE, mRNAArray = TRUE,
mRNASeqType = "normalized", miRNASeq = TRUE, exonRNASeq = TRUE,
RPPAArray = TRUE, Methylation = TRUE, MethylationType = "450K",
GeneMutation = TRUE, SomaticMutation = TRUE)

# 2 only choose 'LUAD' and its clinical data
getTCGAdata(project = "LUAD")
## Not run: 
###### download datasets

# 3 download clinical datasets of LUAD and LUSC
getTCGAdata(project = c("LUAD", "LUSC"), clinical = TRUE, download = TRUE)

# 4 download clinical, RPPA and gene mutation datasets of LUAD and LUSC
# getTCGAdata(project = c("LUAD", "LUSC"), clinical = TRUE, RPPAArray = TRUE, GeneMutation = TRUE)

## End(Not run)

Get hosts of XenaHub object

Description

Get hosts of XenaHub object

Usage

hosts(x)
hosts(x)

Arguments

`x`	a XenaHub object

Value

a character vector contains hosts

Examples

xe = XenaGenerate(subset = XenaHostNames == "tcgaHub"); hosts(xe)
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub"); hosts(xe)

Get Samples of a XenaHub object according to 'by' and 'how' action arguments

Description

One is often interested in identifying samples or features present in each data set, or shared by all data sets, or present in any of several data sets. Identifying these samples, including samples in arbitrarily chosen data sets.

Usage

samples(
  x,
  i = character(),
  by = c("hosts", "cohorts", "datasets"),
  how = c("each", "any", "all")
)
samples(
  x,
  i = character(),
  by = c("hosts", "cohorts", "datasets"),
  how = c("each", "any", "all")
)

Arguments

`x`	a XenaHub object
`i`	default is a empty character, it is used to specify the host, cohort or dataset by `by` option otherwise info will be automatically extracted by code
`by`	a character specify `by` action
`how`	a character specify `how` action

Value

a list include samples

Examples

## Not run: 
xe = XenaHub(cohorts = "Cancer Cell Line Encyclopedia (CCLE)")
# samples in each dataset, first host
x = samples(xe, by="datasets", how="each")[[1]]
lengths(x)        # data sets in ccle cohort on first (only) host

## End(Not run)
## Not run: 
xe = XenaHub(cohorts = "Cancer Cell Line Encyclopedia (CCLE)")
# samples in each dataset, first host
x = samples(xe, by="datasets", how="each")[[1]]
lengths(x)        # data sets in ccle cohort on first (only) host

## End(Not run)

Show TCGA data structure by Project ID or ALL

Description

This can used to check if data type or file type exist in one or more projects by hand.

Usage

showTCGA(project = "all")
showTCGA(project = "all")

Arguments

project

a character vector. Can be "all" or one or more of TCGA Project IDs.

Value

a data.frame including project data structure information.

Author(s)

Shixiang Wang [email protected]

Examples


showTCGA("all")

showTCGA("all")

Convert camel case to snake case

Description

Convert camel case to snake case

Usage

to_snake(name)
to_snake(name)

Arguments

name

a character vector

Value

same length as name but with snake case

Examples

to_snake("sparseDataRange")
to_snake("sparseDataRange")

UCSC Xena Default Hosts

Description

Return Xena default hosts

Usage

xena_default_hosts()
xena_default_hosts()

Value

A character vector include current defalut hosts

Author(s)

Shixiang Wang [email protected]

View Info of Dataset or Cohort at UCSC Xena Website Using Web browser

Description

This will open dataset/cohort link of UCSC Xena in user's default browser.

Usage

XenaBrowse(x, type = c("dataset", "cohort"), multiple = FALSE)
XenaBrowse(x, type = c("dataset", "cohort"), multiple = FALSE)

Arguments

`x`	a XenaHub object.
`type`	one of "dataset" and "cohort".
`multiple`	if `TRUE`, browse multiple links instead of throwing error.

Examples


XenaGenerate(subset = XenaHostNames == "tcgaHub") %>%
  XenaFilter(filterDatasets = "clinical") %>%
  XenaFilter(filterDatasets = "LUAD") -> to_browse

XenaGenerate(subset = XenaHostNames == "tcgaHub") %>%
  XenaFilter(filterDatasets = "clinical") %>%
  XenaFilter(filterDatasets = "LUAD") -> to_browse

Xena Hub Information

Description

This data.frame is very useful for selecting datasets fastly and independent on APIs of UCSC Xena Hubs.

Format

A tibble.

Source

Generated from UCSC Xena Data Hubs.

Examples

data(XenaData)
str(XenaData)
data(XenaData)
str(XenaData)

Get or Update Newest Data Information of UCSC Xena Data Hubs

Description

Get or Update Newest Data Information of UCSC Xena Data Hubs

Usage

XenaDataUpdate(saveTolocal = TRUE)
XenaDataUpdate(saveTolocal = TRUE)

Arguments

saveTolocal

logical. Whether save to local R package data directory for permanent use or Not.

Value

a data.frame contains all datasets information of Xena.

Author(s)

Shixiang Wang [email protected]

Examples

## Not run: 
XenaDataUpdate()
XenaDataUpdate(saveTolocal = TRUE)

## End(Not run)
## Not run: 
XenaDataUpdate()
XenaDataUpdate(saveTolocal = TRUE)

## End(Not run)

Download Datasets from UCSC Xena Hubs

Description

Avaliable datasets list: https://xenabrowser.net/datapages/

Usage

XenaDownload(
  xquery,
  destdir = tempdir(),
  download_probeMap = FALSE,
  trans_slash = FALSE,
  force = FALSE,
  max_try = 3L,
  ...
)
XenaDownload(
  xquery,
  destdir = tempdir(),
  download_probeMap = FALSE,
  trans_slash = FALSE,
  force = FALSE,
  max_try = 3L,
  ...
)

Arguments

`xquery`	a tibble object generated by XenaQuery function.
`destdir`	specify a location to store download data. Default is system temp directory.
`download_probeMap`	if `TRUE`, also download ProbeMap data, which used for id mapping.
`trans_slash`	logical, default is `FALSE`. If `TRUE`, transform slash '/' in dataset id to '__'. This option is for backwards compatibility.
`force`	logical. if `TRUE`, force to download data no matter whether files exist. Default is `FALSE`.
`max_try`	time limit to try downloading the data.
`...`	other argument to `download.file` function

Value

a tibble

Author(s)

Shixiang Wang [email protected]

Examples

## Not run: 
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
hosts(xe)
xe_query = XenaQuery(xe)
xe_download = XenaDownload(xe_query)

## End(Not run)
## Not run: 
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
hosts(xe)
xe_query = XenaQuery(xe)
xe_download = XenaDownload(xe_query)

## End(Not run)

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,
  ...
)
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 [email protected]

Examples

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

Generate and Subset a XenaHub Object from 'XenaData'

Description

Generate and Subset a XenaHub Object from 'XenaData'

Usage

XenaGenerate(XenaData = UCSCXenaTools::XenaData, subset = TRUE)
XenaGenerate(XenaData = UCSCXenaTools::XenaData, subset = TRUE)

Arguments

`XenaData`	a `data.frame`. Default is `data(XenaData)`. The input of this option can only be `data(XenaData)` or its subset.
`subset`	logical expression indicating elements or rows to keep.

Value

a XenaHub object.

Author(s)

Shixiang Wang [email protected]

Examples

# 1 get all datasets
XenaGenerate()
# 2 get TCGA BRCA
XenaGenerate(subset = XenaCohorts == "TCGA Breast Cancer (BRCA)")
# 3 get all datasets containing BRCA
XenaGenerate(subset = grepl("BRCA", XenaCohorts))
# 1 get all datasets
XenaGenerate()
# 2 get TCGA BRCA
XenaGenerate(subset = XenaCohorts == "TCGA Breast Cancer (BRCA)")
# 3 get all datasets containing BRCA
XenaGenerate(subset = grepl("BRCA", XenaCohorts))

Generate a XenaHub Object

Description

It is used to generate original XenaHub object according to hosts, cohorts, datasets or hostName. If these arguments not specified, all hosts and corresponding datasets will be returned as a XenaHub object. All datasets can be found at https://xenabrowser.net/datapages/.

Usage

XenaHub(
  hosts = xena_default_hosts(),
  cohorts = character(),
  datasets = character(),
  hostName = c("publicHub", "tcgaHub", "gdcHub", "icgcHub", "toilHub", "pancanAtlasHub",
    "treehouseHub", "pcawgHub", "atacseqHub", "singlecellHub", "kidsfirstHub")
)
XenaHub(
  hosts = xena_default_hosts(),
  cohorts = character(),
  datasets = character(),
  hostName = c("publicHub", "tcgaHub", "gdcHub", "icgcHub", "toilHub", "pancanAtlasHub",
    "treehouseHub", "pcawgHub", "atacseqHub", "singlecellHub", "kidsfirstHub")
)

Arguments

`hosts`	a character vector specify UCSC Xena hosts, all available hosts can be found by `xena_default_hosts()` function. `hostName` is a more recommend option.
`cohorts`	default is empty character vector, all cohorts will be returned.
`datasets`	default is empty character vector, all datasets will be returned.
`hostName`	name of host, available options can be accessed by `.xena_hosts` This is an easier option for user than `hosts` option. Note, this option will overlap `hosts`.

Value

a XenaHub object

Author(s)

Shixiang Wang [email protected]

Examples

## Not run: 
#1 query all hosts, cohorts and datasets
xe = XenaHub()
xe
#2 query only TCGA hosts
xe = XenaHub(hostName = "tcgaHub")
xe
hosts(xe)     # get hosts
cohorts(xe)   # get cohorts
datasets(xe)  # get datasets
samples(xe)   # get samples

## End(Not run)
## Not run: 
#1 query all hosts, cohorts and datasets
xe = XenaHub()
xe
#2 query only TCGA hosts
xe = XenaHub(hostName = "tcgaHub")
xe
hosts(xe)     # get hosts
cohorts(xe)   # get cohorts
datasets(xe)  # get datasets
samples(xe)   # get samples

## End(Not run)

Class XenaHub

Description

a S4 class to represent UCSC Xena Data Hubs

Slots

hosts: hosts of data hubs
cohorts: cohorts of data hubs
datasets: datasets of data hubs

Prepare (Load) Downloaded Datasets to R

Description

Prepare (Load) Downloaded Datasets to R

Usage

XenaPrepare(
  objects,
  objectsName = NULL,
  use_chunk = FALSE,
  chunk_size = 100,
  subset_rows = TRUE,
  select_cols = TRUE,
  callback = NULL,
  comment = "#",
  na = c("", "NA", "[Discrepancy]"),
  ...
)
XenaPrepare(
  objects,
  objectsName = NULL,
  use_chunk = FALSE,
  chunk_size = 100,
  subset_rows = TRUE,
  select_cols = TRUE,
  callback = NULL,
  comment = "#",
  na = c("", "NA", "[Discrepancy]"),
  ...
)

Arguments

`objects`	a object of character vector or data.frame. If `objects` is data.frame, it should be returned object of XenaDownload function. More easier way is that objects can be character vector specify local files/directory and download urls.
`objectsName`	specify names for elements of return object, i.e. names of list
`use_chunk`	default is `FALSE`. If you want to select subset of original data, please set it to `TRUE` and specify corresponding arguments: `chunk_size`, `select_direction`, `select_names`, `callback`.
`chunk_size`	the number of rows to include in each chunk
`subset_rows`	logical expression indicating elements or rows to keep: missing values are taken as false. `x` can be a representation of data frame you wanna do subset operation. Of note, the first colname of most of datasets in Xena will be set to "sample", you can use it to select rows.
`select_cols`	expression, indicating columns to select from a data frame. 'x' can be a representation of data frame you wanna do subset operation, e.g. `select_cols = colnames(x)[1:3]` will keep only first to third column.
`callback`	a function to call on each chunk, default is `NULL`, this option will overvide operations of subset_rows and select_cols.
`comment`	a character specify comment rows in files
`na`	a character vectory specify `NA` values in files
`...`	other arguments transfer to `read_tsv` function or `read_tsv_chunked` function (when `use_chunk` is `TRUE`) of `readr` package.

Value

a list contains file data, which in way of tibbles

Author(s)

Shixiang Wang [email protected]

Examples

## Not run: 
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
hosts(xe)
xe_query = XenaQuery(xe)

xe_download = XenaDownload(xe_query)
dat = XenaPrepare(xe_download)

## End(Not run)
## Not run: 
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
hosts(xe)
xe_query = XenaQuery(xe)

xe_download = XenaDownload(xe_query)
dat = XenaPrepare(xe_download)

## End(Not run)

Query URL of Datasets before Downloading

Description

Query URL of Datasets before Downloading

Usage

XenaQuery(x)
XenaQuery(x)

Arguments

`x`	a XenaHub object

Value

a data.frame contains hosts, datasets and url

Author(s)

Shixiang Wang [email protected]

Examples

xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
hosts(xe)
## Not run: 
xe_query = XenaQuery(xe)

## End(Not run)
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
hosts(xe)
## Not run: 
xe_query = XenaQuery(xe)

## End(Not run)

Query ProbeMap URL of Datasets

Description

If dataset has no ProbeMap, it will be ignored.

Usage

XenaQueryProbeMap(x)
XenaQueryProbeMap(x)

Arguments

`x`	a XenaHub object

Value

a data.frame contains hosts, datasets and url

Author(s)

Shixiang Wang [email protected]

Examples

xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
hosts(xe)
## Not run: 
xe_query = XenaQueryProbeMap(xe)

## End(Not run)
xe = XenaGenerate(subset = XenaHostNames == "tcgaHub")
hosts(xe)
## Not run: 
xe_query = XenaQueryProbeMap(xe)

## End(Not run)

Scan all rows according to user input by a regular expression

Description

XenaScan() is a function can be used before XenaGenerate().

Usage

XenaScan(
  XenaData = UCSCXenaTools::XenaData,
  pattern = NULL,
  ignore.case = TRUE
)
XenaScan(
  XenaData = UCSCXenaTools::XenaData,
  pattern = NULL,
  ignore.case = TRUE
)

Arguments

`XenaData`	a `data.frame`. Default is `data(XenaData)`. The input of this option can only be `data(XenaData)` or its subset.
`pattern`	character string containing a regular expression (or character string for `fixed = TRUE`) to be matched in the given character vector. Coerced by `as.character` to a character string if possible. If a character vector of length 2 or more is supplied, the first element is used with a warning. Missing values are allowed except for `regexpr`, `gregexpr` and `regexec`.
`ignore.case`	if `FALSE`, the pattern matching is case sensitive and if `TRUE`, case is ignored during matching.

Value

a data.frame

Examples


x1 <- XenaScan(pattern = "Blood")
x2 <- XenaScan(pattern = "LUNG", ignore.case = FALSE)

x1 %>%
  XenaGenerate()
x2 %>%
  XenaGenerate()
x1 <- XenaScan(pattern = "Blood")
x2 <- XenaScan(pattern = "LUNG", ignore.case = FALSE)

x1 %>%
  XenaGenerate()
x2 %>%
  XenaGenerate()

Package 'UCSCXenaTools'

Help Index

Get or Check TCGA Available ProjectID, DataType and FileType

Description

Usage

Arguments

Author(s)

Examples

Get cohorts of XenaHub object

Description

Usage

Arguments

Value

Examples

Get datasets of XenaHub object

Description

Usage

Arguments

Value

Examples

Easily Download TCGA Data by Several Options

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Fetch Data from UCSC Xena Hosts

Description

Usage

Arguments

Details

Value

Functions

Examples

Get TCGA Common Data Sets by Project ID and Property

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Get hosts of XenaHub object

Description

Usage

Arguments

Value

Examples

Get Samples of a XenaHub object according to 'by' and 'how' action arguments

Description

Usage

Arguments

Value

Examples

Show TCGA data structure by Project ID or ALL

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Convert camel case to snake case

Description

Usage

Arguments

Value

Examples

UCSC Xena Default Hosts

Description

Usage

Value

Author(s)

See Also

View Info of Dataset or Cohort at UCSC Xena Website Using Web browser

Description

Usage