XenaPrepare: Prepare (Load) Downloaded Datasets to R

In ShixiangWang/UCSCXenaTools: Download and Explore Datasets from UCSC Xena 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]"),
  ...
)

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 [e-mail]

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)

ShixiangWang/UCSCXenaTools documentation built on Jan. 17, 2024, 2:19 a.m.